Annabeth first appears after Percy wakes up from his fight with the Minotaur the night before. She was nursing him back to health and quickly asked him if he knew anything about the Summer Solstice and what was stolen. However, Percy was still confused and didn't know what she was talking about. When someone knocked on the door, Annabeth filled Percy's mouth with a spoon full of pudding and Percy fell back to sleep. Percy didn't actually learn her name until Grover took Percy to see Mr. D and Chiron called Annabeth over and asked her to make sure his bunk in Cabin 11 was ready. Instead of commenting about how cool he was like he thought, Annabeth told Percy that he drooled in his sleep before heading off to the cabin. Percy then met her out front of Cabin 11 and saw she was reading an architecture book in Greek. When Percy entered the cabin, he was asked if he was regular or undetermined, to which Annabeth answered that he was undetermined. When Luke Castellan, the cabin leader, welcomed Percy, Annabeth began to blush but hid it when Percy noticed.

Annabeth quickly dragged Percy from the cabin and begins to get mad at him. She insults herself for thinking that Percy was the one she was waiting for and explains that any other demigod would have loved the chance to fight the Minotaur. She also explains to him how monsters never really die, as they will eventually reform in Tartarus. When Percy questions why he can't just pick a cabin, like one of the empty ones, which are Zeus' Cabin, Poseidon's Cabin, Hera's cabin, and Artemis' Cabin, she explains that the cabin depends on who the demigod's dad/mom is. When Percy says that his father is dead, Annabeth says he isn't dead or Percy wouldn't be at Camp Half-Blood. When Percy tries to deny this, Annabeth correctly guesses that Percy had been kicked out of a lot of schools, moved around a lot, he has Dyslexia, and most likely ADHD. Before she can go on, Clarisse La Rue interrupts and Annabeth introduces her. When she tries to initiate Percy into the camp, Percy gives Annabeth the Minotaur's horn, but he is quickly overpowered by Clarisse. Annabeth watched through her fingers as Clarisse almost dunked his head in the bathroom toilets, but Percy controlled the water to force Clarisse out the door. Annabeth was also soaked, but she wasn't forced out. She then commented that she wanted Percy on her team for Capture the Flag. She then showed him the rest of the camp before leaving to train and saying that she would ask Chiron to allow Percy to see the Oracle, showing interest in getting her own quest and having some knowledge of a possible war among the gods.

Later when talking to Luke about people saying he was Big Three material and Annabeth calling him the one she was waiting for, Luke said that Chiron was given a prophecy by the Oracle saying that Annabeth wouldn't be ready for a quest until a certain someone arrived at camp. He also mentioned that Annabeth acted like that to every new camper. Percy saw her later at dinner with the rest of Athena's Cabin. Percy from then on took Ancient Greek with Annabeth and learned other self-defense type classes. While the cabins prepared for Capture the Flag, Annabeth and two of her siblings came in with the banner of Athena as their flag, while Clarisse and her siblings came in with the banner of Ares.

During the game, Annabeth lead the blue team and used Percy as bait for Clarisse, knowing she would want revenge on him. After Percy managed to defeat Clarisse, Annabeth took off her invisibility cap to show she had been there. While Percy was annoyed at her for using him, she claimed she was about to jump in, but Percy managed to handle it on his own. When Annabeth notices the wound in his shoulder healing as he stood in the water, she quickly figures out that Percy is a son of Poseidon, but had assumed that Zeus would have been the one to break the oath. Before she can explain it to him, a hellhound attacked. Annabeth stepped in front of the monster, but it jumped over her to attack Percy. The hellhound was quickly defeated, but not before injuring Percy. Annabeth told the others to put Percy in the water, which quickly healed his wounds and Annabeth pointed out the symbol of Poseidon hovering above Percy's head.

Later, after Percy visits the Oracle and gets a prophecy, Chiron explains that the gods are on the brink of war because Zeus' Master Bolt had been stolen and is blaming Poseidon for it. When Grover Underwood volunteers to help in the quest, Annabeth quickly takes off her cap and volunteers as well, revealing she had heard the entire conversation. She claims that while Athena and Poseidon aren't on the best of terms, she is the best person for preventing him from messing up, calling Percy "Seaweed Brain." The next morning, Annabeth got ready for the quest by bringing her cap, her knife, and was given some supplies by the camp before leaving for New York City. Before leaving, Luke gave Percy a pair of winged shoes and gave Annabeth a goodbye hug, which almost made her pass out.

After being driven into the city by Argus, they are quickly found by the Furies while taking a bus to New Jersey. Annabeth used her cap to hide Percy from them in hopes that Percy's smell will hide her and Grover's sent. Percy snuck past them, but the Furies went after Annabeth, violently demanding to know where "it" is. Percy hit the brakes and the bus crashes due to the fighting between the demigods and the Furies. The three escape and Annabeth wonders what the it the Furies wanted was, as if they were talking about Percy, they would have said he. However, being tired and without a ride, they find their way to Aunty Em's Gnome Emporium. While Percy and Grover quickly fall for Aunty Em's kindness, Annabeth becomes suspicious and soon realizes that the old woman is Medusa moments before they were all turned to stone. Annabeth becomes extremely worried because it was her mother that turned her into a monster because she was caught kissing Poseidon in one of her temples. She instantly warned them to look away before turning invisible and pushing Grover and Percy over. During the fight, Annabeth convinces Percy to kill her as she knows he has the better weapon and because Medusa hates her and her mother, Athena. After Percy killed Medusa, Annabeth walked up to it and covered the head in a dark veil so they wouldn't see it's eyes. Percy then ships Medusa's Head to Mount Olympus.

While camping in the woods, Percy figures out that Grover was the satyr that tried to get Annabeth, Thalia, and Luke back safely, but ultimately failed. The next morning, Annabeth woke Percy up and made the group breakfast, while Grover found a lost dog that they could return for the reward money, allowing them to buy train tickets to St. Louis, Missouri. During the trip, Annabeth asked Percy (who had a dream about Kronos) who he won't help, as he said that in his sleep. Percy explained the dream, and Annabeth began to have doubts that Hades was the one that took the Master Bolt as everyone had originally thought. She also told him he couldn't make deals with Hades, but Percy asked her what would happen if Hades took her father. This angers Annabeth and she explodes, saying she would leave her dad to rot and revealing a little about her past in the process, saying she hated her family, despite keeping her dad's ring. However, as soon as she sees the Gateway Arch, she brightens up and reveals that she hopes to one day become an architect and building something that would last for a thousand years. Once in the station, Annabeth took Percy and Grover to the Gateway Arch and got to the top shortly before closing time. While at the top, a large woman with a small dog asked about their parents, to which Annabeth told her that they were scared of heights. Shortly after, Annabeth went downstairs with Grover and waited for Percy, not knowing the danger he was in. They watched as Percy fell from the arch in an explosion and landed in the nearby river. Annabeth and Grover ran to him, with Annabeth trying to look mad, but really being relieved that he was not harmed.

After getting on a train out of the city, they arrive in Denver and Annabeth showed Percy how to Iris Message. They get a hold of Luke instead of Chiron, and he informs them that the camp is becoming a battle field with cabins picking sides in an upcoming war. Annabeth on the other hand messes with her hair and tried to make herself look prettier for Luke, however the connection is cut short soon after. While at a diner, Ares appeared before them and offers them a ride west if they get something for him in Waterland. Percy and Annabeth are reluctant because the item is in the Thrill Ride O' Love and neither feel comfortable. Once they are inside, a trap made by Hephaestus is activated and hundreds of thousands of metal spiders flood the room and Annabeth is paralyzed with fear. Percy floods the room with water from the pipes and they sail toward the exit, but the gate is closed. Annabeth uses her brain to figure out when the best time to jump was and they make it out safely (Percy noting that if they jumped when he thought they should, they would have smashed against the gate). When they return the item, Ares allows them to climb into the back of a Kindness International truck, which transported animals.

While in the truck, the find that Kindness International are smuggling animals and they try their best to help the animals. Annabeth and Grover tell Percy the full story of how they made it to camp and how Thalia sacrificed herself. Annabeth also says that she doesn't blame Grover for what happened and neither did Thalia, also calling him the bravest satyr she knew. After Grover fell asleep, Annabeth talks about the beads on her necklace and eventually opened up about her rocky relationship with her father, explaining the ring on it. When Percy asked her if she would side with her mother if she went to war against Poseidon like they did during the Trojan War, Annabeth told him that she would side with him as they are friends. The next morning when Maurice went to go feed the animals, Annabeth put on her cap and started banging on the outside, distracting the driver long enough for Percy and Grover to free the animals.

While in Las Vegas, they eventually arrive at the Lotus Hotel and Casino where they are given key cards and decide to have spend the night and play some games while they're there. Annabeth gets really into an architecture game and can't bring herself to pull herself away, even after Percy tells her it is a trap. She doesn't budge until the word "spider" is said and she comes to her senses.

Once arriving in Los Angeles, Annabeth, Percy, and Grover are chased into Crusty's Water Bed Palace, where Annabeth and Grover are quickly trapped by a monster called Procrustes, who stretches out anyone to the exact length of the bed. While Annabeth pleads for Percy to help her, he is forced to outsmart the monster and eventually traps him in one of his own beds, freeing Annabeth in the process. Percy then grabs the address from Procrustes' address book and the three head to DOA Recording Studios, the entrance to the Underworld.

Once reaching the Underworld, they couldn't think of a way to get to Hades without passing Cerberus, until Annabeth pulled out a rubber ball and began to play fetch with him and claiming she used to train a Doberman. She played fetch long enough for Percy and Grover to pass by and then followed them telling Cerberus she would play with him again sometime and he whined as she left. After passing the large dog, Grover's shoes began to act up and began pulling him toward Tartarus, the deepest part of the Underworld. While thinking he was only messing around, Annabeth quickly jumped to action along with Percy as they pulled him. Annabeth suggested they untie the shoes, but Grover was only saved when his fake feet fell off and the shoes flew into the pit. Annabeth, knowing what the pit was suggested they all back away as soon as possible.

When they arrived at Hades' Palace, Annabeth was respectful to Hades and informed him of a war approaching among the gods, but Percy quickly asked for the Master Bolt back from him. Hades erupts into anger at this, claiming that Percy not only took the Master Bolt, but his Helm of Darkness as well. Annabeth tried her best to figure out what all this meant, but failed to see the connections. When the Master Bolt appeared in Percy's backpack, Annabeth becomes even more confused. Percy pulled out three pearls that his father had given him to escape the Underworld, and Annabeth offered to stay so Sally Jackson could go. Eventually, Grover, Annabeth, and Percy returned, leaving Percy's mom behind. Once back on the surface, Annabeth apologizes for leaving Sally behind.

However, Ares soon appeared and revealed that he was the one that hid the bolt in the backpack, and the one that wanted the gods to go to war. Percy challenged Ares to a fight, much to Annabeth's protests, but she gave him her necklace for luck. Annabeth watched the battle with Grover and warned them when policemen had arrived, but Ares caused a wall of fire to appear in front of them. When Percy managed to get Ares to retreat, Annabeth warned Percy not to look at Ares' Divine Form. After taking the Helm of Darkness from Ares and giving it to the Furies, Annabeth and Percy both figured out what was in the pit.

The three flew back to New York and Percy sent Annabeth and Grover back to Camp Half-Blood to tell Chiron what had happened and because if the gods didn't believe Percy's story, he wanted to keep them away from danger. After the Master Bolt was returned to Mount Olympus and all seemed well, Percy returned to camp and celebrated a successful quest with Annabeth and Grover around the campfire. They even set up a picnic as Grover left to go search for the lost god Pan, with Annabeth giving him a goodbye hug. However, when Percy was poisoned by Luke and revealed himself to be an agent of Kronos, Percy woke up the next morning in the Big House with Annabeth tending to him once again, mirroring Percy's first arrival at camp. He explained what had happened with Luke, causing Annabeth to become shocked and then angry at him, cursing his name. Annabeth then spends her time helping Percy recover and admits that she will spend a year with her dad, as she had sent a letter to him shortly after arriving at camp. Percy and Annabeth then say their goodbyes, calling the other Wise Girl and Seaweed Brain respectively.

The ship they arrive on is the Princess Andromeda. A monster ship with Luke on it and they are forced to escape. Annabeth leads them to an old hideout used by her, Luke, and Thalia. She also tells Percy after sending Tyson outside why she hates cyclopes, until Tyson comes back with a hydra nearby. After battling the hydra with little effect, Clarisse arrives and takes them with her to the Sea of Monsters. After entering the sea, Percy and Annabeth are split up from everyone else when Clarisse's submarine explodes and arrive at C.C.'s Spa and Resort. While Annabeth is given a full makeover, Percy is turned into a guinea pig. Annabeth outsmarts Circe and uses one of Hermes' multivitamins to turn Percy back and make them immune to magic for a short time. She then puts her knife to Circe's neck, and threatens her. They escape using Blackbeard's ship. Annabeth hears the Sirens' song while on the boat, and although she'd convinced Percy to tie her to the mast, he forgot to disarm her (celestial bronze knife) and she got hypnotized by the song. It is confirmed that her fatal flaw is hubris (pride), being a child of Athena.

They eventually make it to Polyphemus' island where Grover and Clarisse are being held captive (and finding Tyson along the way). In order to provide a distraction, she puts on her invisible Yankees cap and tells the cyclops she is "Nobody," angering him to no end as he smashes rocks and stops around, eventually capturing her. She is freed when Percy tells Polyphemus he is "Nobody," since Annabeth was a girl. He lets he go and Percy manages to defeat his half brother and take the fleece. They all eventually sail out of the Sea of Monsters and Annabeth and Percy give Clarisse enough money for a plane ticket back to camp. After she leaves, they are attacked by Luke for the fleece, but when he finds out they don't have it, Annabeth is forced to watch Luke and Percy fight each other. Percy manages to trick Luke into revealing he poisoned Thalia's Tree by sending an Iris Message to Camp Half-Blood behind Luke and getting him to admit he did it, proving that Chiron was innocent. Chiron and the Party Ponies come to their rescue and they return to camp.

Annabeth and Percy teamed up to win the chariot race waged between the cabins of the camp. Following their victory, Annabeth's perpetual facade of calm cracked slightly when she kissed Percy on the cheek. Afterward, while Annabeth is doing patrol for the camp, the fleece's magic works too well, causing Thalia's pine tree to 'give back' Thalia's spirit, causing Thalia to come back to life (though she wasn't really dead).

Later, Percy has another dream where Annabeth is still holding the sky and in order to trap Artemis, he tells her that if she doesn't take the sky from Annabeth, she will surely die from the weight. Artemis takes the sky and Annabeth falls to the ground and carried away by Luke who decides to use her as bait for the other demigods.The Oracle of Delphi gave one of her ever-cryptic prophecies, and off went Percy, Thalia, Grover, Bianca di Angelo (a young Hunter whom Percy, Annabeth and Thalia were attempting to recruit along with her brother Nico di Angelo when Annabeth was taken) and the Huntress, Zoë Nightshade, in pursuit of Artemis and Annabeth and the monster which Artemis was chasing after. Aphrodite, Goddess of Love and Beauty, convinced Percy that his love for Annabeth was worthwhile, though she also made it incredibly harder for them to fall in love. Though Percy was originally not included in the quest, Nico pleaded to him and convinced him to follow them to protect his sister, Bianca. He was seemingly unable to leave the fate of his best friend in the hands of others. After a prolonged quest, which included the loss of Bianca di Angelo in the Junkyard of the Gods battle to a prototype of Talos made by the forge god Hephaestus, the group arrived at the ruins of the Titans' palace, Mount Othrys in San Francisco, California, and found Annabeth, with a grey streak in her hair as a result of holding the sky and Artemis, who was struggling under the weight of the sky; both captives of Luke and Atlas.

Upon the re-imprisonment of the Titan General Atlas, the death of Zoë, and the apparent death of Luke (or so they thought, except Annabeth), Annabeth was saved by Percy and the others, along with her mortal father, Frederick Chase who attacked the monsters chasing the group using the celestial bronze bullets that he had made from things Annabeth had left behind when she ran away from home. Also, Annabeth's stepmother shows care for Annabeth in this book when she tells Percy that even though she knows that Annabeth is a demigod and can't live in San Francisco because of Mount Orthys, the Titan base camp, she still has a home with them and can come anytime she wants.

Annabeth is now 14 years old. She and Percy were supposed to go to the movies after his orientation day into his new school, Goode. However, their plans are interrupted when Percy blows up part of the school in a fight with some monsters, Kelli and Tammi, who were empousai in the forms of cheerleaders. Her possessiveness for Percy is revealed when she becomes annoyed at him after she finds him escaping with the mortal girl Rachel Elizabeth Dare. She has a fight with Percy and refuses to speak to him during the Gray Sisters' Taxi journey to Camp Half Blood. Once back at camp, Percy and Annabeth accidentally discover an entrance to the Labyrinth under the rock pile known as Zeus's Fist while on a camp game designed personally by Quintus who is discovered to be Daedalus later on, the inventor and the creator of the Labyrinth. She realizes that Luke can use this entrance to invade the camp at any moment unexpected. Annabeth leads the quest into the Labyrinth, fulfilling one of her many ambitions at last. While studying the Labyrinth, Percy walks in on her. Annabeth was frustrated and held out her arms so Percy could give her a hug. He remarks that her hair smelled like lemon soap.

Later, Annabeth descends into the Labyrinth with Percy, Grover, and Tyson (Percy's half brother and a very good cyclops) to find a way to stop Kronos' evil forces from invading the borders of Camp Half-Blood by searching for its inventor, Daedalus. The Oracle of Delphi gave her a prophecy which appears to have scared her and she refuses to say the last line. As they go into the Labyrinth, they face and fight many monsters. Annabeth faces a Sphinx and finds its riddles (which were actually factual questions) not challenging enough and an insult to her intellect. They escape the claws of the Sphinx and continue on to find Hephaestus in one of his many forges so he can tell them about where to find Daedalus and his workshop in the Labyrinth. Annabeth believes that Percy will die when Mount Saint Helens erupts but right before he goes in she kisses him for good luck.

Percy was instead marooned on the phantom island of Ogygia when he tried his best to fight the telekhines, half-dog half-monsters, who were perpetrating Hephaestus's once favorite of all of his many forges, where the sad but seductive Calypso resides. When Annabeth sees Percy return (while she is burning his shroud, believing him to be dead) she hugs him fiercely, but quickly lets go when she realizes she is making a big scene in front of all the other campers. When she finds out what happened to Percy after he tells her and Chiron in Chiron's office in the Big House, Annabeth angrily exits after guessing where he was stranded and obviously feeling jealous. Percy asks mortal Rachel Elizabeth Dare, much to Annabeth's dismay. Annabeth makes several offending remarks toward Rachel, who simply shrugs them off and after a long while, Annabeth accepts her as their guide. The three of them discover Luke, who has become Kronos' vessel. After the Battle of the Labyrinth from the entrance of the Labyrinth under Zeus's Fist in the woods, Luke and his army are forced back into the Labyrinth, leaving after causing many, but only two named, casualties.

Annabeth joins forces with the campers and goes to New York City to save Manhattan and Mount Olympus (over the Empire State Building) itself from Kronos' Titan army in the Battle of Manhattan. At one point, she takes a poisoned knife for Percy, that Ethan Nakamura was using to try to stab him. Even though she does know Percy was invincible, Annabeth jumps in the way and takes the stab, defenseless. It is later revealed that if she hadn't taken the dagger for Percy, he would have died, because his only weak spot, the small of his back, was Ethan's target though it is unknown how Ethan knew about the weak spot it or Ethan may have not been aiming for any spot in particular as he told Kronos. Percy gets Blackjack, his black pegasus, to fly her away, takes Kronos on, and is forced to retreat. When Percy checks on Annabeth, he decides to tell her where his Achilles heel is. Annabeth is the only person that knows where it is besides Percy. While Annabeth is resting because of the poisoned knife, she tells Percy that Luke had visited her before they went into the Labyrinth, explaining why Hermes, the messenger of the gods, the patron of thieves, and others, was mad at her for not saving Luke when she had the chance to, and she also states that Percy looks "cute" when he is worried. When it is discovered that Silena was the spy, Percy Jackson describes Annabeth looking as if "The world had just been pulled from underneath her feet."

Annabeth saves Percy and Olympus by finally realizing for whom the prophecy is truly meant for: Luke. She tells Percy to give Luke her knife (that was Luke's gift to her when she was seven) so he can stab himself, which would banish Kronos back to Tartarus though there is no evidence to where the spirit of Kronos went to after Luke sacrificed himself since they were up high above Manhattan in the Hall of the Gods in the Olympian gods' throne room on Olympus. Annabeth is rewarded by the gods (actually by her own mother Athena), now being able to fulfill her dream and design for the gods a new city on Olympus, as the old one was ruined by the battle (actually destroyed by Kronos when he invaded Olympus through the Empire State Building, entrance to Olympus). She is also allowed to design the new cabins at Camp Half-Blood.

She and Percy celebrate his 16th birthday privately, in the apparently empty dining pavilion of Camp Half-Blood. Percy attempts to tell her that he has strong feelings for her, but she is amused, up until the point he states that she is not making it easy for him to admit it. She laughs and warns him that she will never, ever make things easy for him, and that he should get used to it, wraps her arms around his neck, and kisses him. Percy said that it felt like his brain was melting through his body, and that he could have stayed like that forever, until Clarisse La Rue and several other nosy campers eavesdrop on the whole episode and throw Percy and Annabeth into the camp's canoe lake. However, Percy creates an air bubble deep under the surface of the lake, because he is a son of Poseidon, and they share, as Percy describes it, "the best underwater kiss of all time." At the end, Percy is relieved that Annabeth is staying in New York and they leave Camp Half-Blood together.

While celebrating their one month anniversary, Annabeth asked Percy what he had planned for their special dinner that night. Percy, who never remembered promising something like that, stalled for time just as Hermes arrived. Annabeth and Hermes get into a small fight, which is quickly broken up by Percy who drags Hermes into his delivery truck to talk. When they exit, Annabeth quickly figures out that someone stole Hermes' caduceus. Annabeth takes out her Video Shield and finds that the giant Cacus is in the meatpacking distract.

When Percy and her get there, they climb down a ladder into the sewers and find an underground cavern. There they meet Cacus and he tried to sell them watches and clothes, which Annabeth quickly notes are fakes. When Percy asked for the caduceus back, Cacus claims he will figure out how it works and become the god of traveling salesmen. Annabeth and Percy go on the attack, with Annabeth stabbing him in the back of the knee and Percy stabbing his leg. However, Cacus backs her and Percy into a corner, destroys her shield, and is about to turn her to stone when George and Martha turn into a cell phone. They escape the cavern when Percy calls thousands of gallons of New York sewage to him and it pushes them to the surface, with Annabeth cursing Percy the entire time.

Annabeth then comes up with a plan and runs to a crane, knowing how to operate it as she observed them on Olympus. Percy lures Cacus under the crane's large hook and Annabeth drops it on his head before picking him up and swinging him into the air, where Percy destroys him with the caduceus' Laser Mode. Percy and Annabeth then return the caduceus to Hermes, who is very grateful. As a reward, Hermes transports them to Paris for a special dinner. They night ends with Percy and Annabeth walking by the river and Annabeth wondering what Percy has planned for their two month anniversary, which makes Percy happy that she sees a future for them in a month.

Annabeth appears in a chariot pulled by pegasi with Butch, a demigod son of Iris, the carrier of messages through rainbow "Iris-messages" for the gods and the rainbow goddess, to pick up the three demigods Jason Grace, son of Jupiter, Piper McLean, daughter of Aphrodite, and Leo Valdez, the son of the forge god, Hephaestus. It is revealed she and Percy are still dating. Annabeth and Butch, went to the Grand Canyon in search for Percy, who has been missing for three days. Annabeth had been receiving visions from Hera, that a hero with one shoe, which she finds out is Jason, will solve her problems, which is finding Percy. She is also shown frustrated and worried with Percy's disappearance. Before leaving the Grand Canyon, Annabeth yells to the sky, "What do you want from me? What have you done with him?" Annabeth gives Piper a tour of Camp Half-Blood, also letting Piper choose her weapon Katoptris, then explaining that Piper's relationship with Jason at the Wilderness School was an illusion due to the Mist and wanting to give Piper a chance to break down privately when she realized the same thing, though she has been holding herself together as well, it is obvious that Annabeth is equally crushed at losing Percy so mysteriously.

When Jason is given his quest to rescue Hera from the capture of Polyphrion the giant, Annabeth refuses to accompany the quest group, partly because the prophecy states that children of Hephaestus, Jupiter/Zeus, and Aphrodite will go instead, and partly out of her own distaste for Hera. Instead, she uses the time they are gone to continue her search for Percy.

After the quest group returns and relates their findings — the rise of the giants, the attempted return of Gaea, and the fact that Jason was "exchanged" to the Greek Camp Half-Blood — Annabeth puts everything together and realizes, as Jason has, that Percy has been taken to the Roman Camp called Camp Jupiter as the corresponding half of the exchange. She vows to accompany Jason, Piper, and Leo when they journey there to retrieve him.

While Percy Jackson is running away from the gorgons, Stheno and Euryale, he sees San Francisco, which reminds him of Annabeth, the only person he can remember from his past. Also, when Percy talked to Lupa, she told him that if he completed his quest, he would see Annabeth again soon.

Before Percy goes on his quest to free Thanatos, he has a dream and sees Annabeth. She tells him to stay at Camp Jupiter because Tyson and Mrs. O'Leary are close by and are trying to find him. When Percy wakes up, he feels bad that he will have to ignore Annabeth and go on the quest anyway as the Roman campers need him. During his quest, Percy has flashes of memory about Annabeth, as when he looked at Mount Tam, he remembered the fight with Atlas and he told Frank and Hazel he had been their once looking for Annabeth. Later when looking for Ella in a library, he said Annabeth would like this place as it was quiet and filled with books. He later remembers that she loved architecture.

After completing the quest, Hera appears to Percy in his dream. She tells him that Annabeth will cause him trouble in the future. When Percy says that Annabeth is the person he most wants watching his back, Hera says "We shall see," and tells Percy that she will have a hard task ahead of her when he arrives in Rome and that she may not be up to it.

The next morning, Percy arrives in the Senate meeting to discuss the arrival of the Argo II, which they will allow to land. As he goes to meet the ship, he says he knows Annabeth is on board and this could be the best day of his life if everything went right.

As Annabeth approaches Camp Jupiter on board the Argo II, she checks the ship to make sure that everything is set up, including the back-up plans to the back-up plans. She tries her best to keep Gleeson Hedge under control, while watching Piper McLean practice her lines for the meeting. When Piper repeats the line for the Romans to lay down their weapons, as the Greeks only wanted to talk, her Charmspeak almost causes Annabeth to lay down her knife, and have a chat. She also watches Leo Valdez fiddle with the controls of the Argo II.

While watching Jason Grace prepare for the meeting, she could not help but not trust Jason, as he always seems too perfect. She thinks maybe he would turn them in as prisoners once they landed and give the ship as a gift. Also, whenever she looks at Jason, she remembers how much she misses Percy. She wishes she could talk to her mother for help, but it was impossible after an encounter a month earlier with her, where Annabeth had received a horrible present. Annabeth also mentions feeling a mysterious chill, as if "an evil snowman had crept up behind her and was peering over her neck."

An explosion nearly knocks Annabeth overboard, and Terminus, the Roman god of boundaries, appears on the Argo II. He shrieks that he will not allow weapons inside the Pomerian Line. Annabeth tries to regain control of the situation and calm everyone down by introducing herself to Terminus, who finds that Annabeth being the daughter of Athena, the Greek form of Minerva, is "scandalous." But before Annabeth can question Terminus on what he means, Jason interrupts and asks for permission to land inside the Pomerian Line.

Annabeth spots Percy Jackson walking with Frank Zhang, "a boy with a black buzz cut" and Hazel Levesque, "a girl wearing a Roman cavalry helmet," like they were best friends. She also notices that he is now a Praetor, which makes her heart do a gymnastics routine.

Annabeth orders Leo to stop the ship as she asks Terminus whether there is a rule against the ship hovering over New Rome. She explains that technically the ship will not be touching Roman soil, and suggests they use a rope ladder to get down to the Forum, promising Terminus that all their weapons will stay on the ship as long as the legion reinforcements will honor the same rules. When questioned by Leo, who asks if this is a good idea, Annabeth clenches her fists to stop them from shaking. She feels a cold presence, which seems to be laughing at her and the bad choices she is making. But she knows Percy is down there, and that she has to see him. She replies, it will be fine and Terminus will make sure that both sides will obey the rules, if Terminus agrees. Terminus sniffs, but agrees to "for now," and allows them to climb down the ladder to New Rome, but pleads them to not destroy his town.

Annabeth descends with the rest of the Argo II's crew where she spots Tyson and Mrs. O'Leary, and Reyna, whom she finds reminding her of herself. Just as Reyna begins to give a welcoming speech, both Percy and Annabeth surge forward and hug and kiss each other, before Annabeth flips him over onto his back as she channels all her bitterness and worry about him into her judo flip. Reyna jokingly asks if Annabeth is actually a Roman or an Amazon before inviting them to their welcome feast. But Annabeth still cannot shake the feeling that something is about to go terribly wrong. They all tell stories of the quests they have been on, and Annabeth is surprised at the revelation that Hazel and Nico are related. Annabeth helps in stopping Octavian from taking Ella the harpy, when she accidentally blurts out a prophecy, by ridiculing Octavian's idea that harpies can tell the future.

While Reyna is walking with Annabeth through New Rome she calls for her dogs, Aurum and Argentum. The girls discuss the differences between Minerva and Athena. Reyna notes there are no children of Minerva at the camp due to Minerva being a virgin goddess, and that if they were to come to Camp Jupiter, they would be artists and not warriors or leaders on quests. Annabeth then realizes that she had met Reyna before at Circe's Island. They walk all the way to the Garden of Bacchus and appreciate the view. Reyna explains that she wanted to talk to Annabeth to learn the truth. Instead of Annabeth feeling bad about her not being able to trust anyone at camp, she talks about her family, growing up, and adventures in Camp Half-Blood.

Throughout the conversation, Reyna mentions that when she was on Circe's Island, she had met a son of Athena who washed up on the shore and was rambling about the Mark of Athena. Then, a large explosion makes a crater in the forum of New Rome. The Argo II then continues to attack the city. Reyna and Annabeth rush down to the Forum. Since Roman's are not allowed any weapons inside the Pomeranian Line, they had started to throw food, rocks, and plates at the Greeks. Piper and Jason try to calm the angry mob by telling them they would never attack New Rome, but fail. Right outside the Pomeranian Line the Roman's were set up catapults to fire on the attacking Argo II.

Annabeth sees Percy using water from a fountain to douse the angry mob of Romans. Octavian comes down the leader screaming that Leo has fired on everyone. Percy asks if Hazel and Frank are coming with them on the ship, and they say yes. Hazel calls for Arion and distracts the crowd by riding straight through it. Frank, in attempt to let Percy and Annabeth climb the rope, changes form into a dragon. Once Percy and Annabeth are up, Leo is tackled to the ground by Percy and falls on his head. Annabeth then takes charge of the ship and leaves Camp Jupiter as quickly as possible.

Annabeth interrogates Leo, but is called down to check on Jason, when she returns Leo tells them that they need emergency supplies to repair the ship and they land near the Great Salt Lake, in Utah. Percy and Annabeth ride Frank, in the form of a dragon, into Salt Lake City to get tar, although they run into some tar monsters, they return safely with a big bucket of tar. The demigods hold a conference in the mess hall, Piper tells them about her visions that she has seen in her knife. Unable to figure out what the visions or prophecies mean, they decide to visit Kansas, where Piper saw a strange man, Bacchus is standing in front of a sign saying 'Topeka 32'.

Leo needs Annabeth to help him repair the hull, but Percy promises to come back to her. When they return, Annabeth and the rest of the crew are surprised when Piper returns on Blackjack with two unconscious demigods. Piper explains what happened; the conversation with Bacchus who told them to go to Atlanta and find Phorcys, the trap sprung by Gaea and the eidolons and both Percy and Jason thank her for saving them. They work out what Gaea wants, the blood of two demigods, one male and one female, to water the stones of Mount Olympus and wake Mother Earth. Piper removes the eidolons from all three boys' bodies, and makes them swear on the River Styx that they will never return to this ship or possess any member of their crew.

In the middle of the night, Annabeth sneaks into Percy's cabin and wakes him up. They go down to the bottom of the ship where the stables are, which reminds her of their first quest when they were traveling in the truck full of zoo animals. Percy asks her why she is nostalgic about that, but she says it was the first time they actually talked, and when she decided to like him. They kiss, and then fall asleep.

The next morning, Frank finds them and is terrified that Coach Hedge is going to kill them for sneaking out, as everyone thought they had been kidnapped. They have a conference and Percy tells them his dream about the twin giants, Otis and Ephialtes, and Nico di Angelo suffocation in a bronze jar.

Percy and Frank decide to find Phorcys, Percy also wants to take Annabeth but Coach Hedge declares that she is grounded. He volunteers himself for the expedition. When the trio return, Annabeth was trying to amuse Hazel by telling her about Percy's greatest 'Seaweed Brain' moments. Leo sets course for Charleston, whilst Percy and Frank tell the demigods what happened, with Hedge interjecting from time to time. They discuss why they are heading to Charleston, to find a map, Percy suggest for 'The Mark of Athena' but Annabeth seems to be projecting a 'I don't want to talk about it' vibe, so Percy doesn't elaborate. Jason tells them that at Charleston, there is a museum full of Confederate ghosts, where he, Leo and Frank volunteer to visit. He also mentions the Battery park near the harbor, where there was a ghost or spirit dressed like a Southern Belle from the Civil War, Reyna went up and talked to it but when she came back she was shaken and never acted the same way around him. Annabeth decides to have a girls' adventure with Piper and Hazel.

Annabeth thinks about the last time she met her mother, in her Roman form as Minerva. Annabeth tries to get her attention by calling her Athena, but the goddess dreamily replies that 'that was my name, before they sacked my city, took my identity, made me this.' Athena tells Annabeth to avenge her, and destroy the Romans because they were dishonorable and copycats. Hera said that they must keep the two camps apart, but Athena wanted them to fight to the death, and for her children to destroy the 'usurpers'. When Annabeth argues back that she understood warfare, and was wise enough not to fight with reason, but Athena replies that now she will never forgive them, and neither would my children. She gives Annabeth a coin that looks like an old-fashioned subway token but when she looks upon it, it becomes an ancient Athenian silver drachma with the symbols of an owl and an olive branch with a Greek inscription on the other side. Athena urges her to 'Follow the Mark of Athena. Avenge me.', when Annabeth tries to explain that Percy is missing and Hera's plan to bring the camps together, the goddess implores her to kill Percy if he has become Roman, and if Annabeth joins them, then she has failed her mother already. No matter how many times, she tried to throw the silver coin away, it kept returning to her pocket like Percy's sword, Riptide. Annabeth thinks she is beginning to understand what her quest is, but prays to the gods that she is wrong.

Frank comes into Annabeth's cabin asking for help as he wants to know how to get out of the Chinese handcuffs, that he took from the Aquarium. Annabeth feels quite honored that Frank was embarrassed but looked for her help, after Leo teased him. She scans the handcuffs onto her laptop which produces a 3-D model on the screen. She shows him the solution to the puzzle, is to not fight against the handcuffs, and that the best traps are the most simple.

Annabeth, Piper and Hazel find the 'ghost' who turns out to Aphrodite, who invites her to have tea and chat, even though, according to her, war is coming and bloodshed is inevitable. Aphrodite reveals that the civil war between the Greeks and Romans doesn't affect her as much as the other gods (who seems to have split personalities), as love is universal. She tells them about why Athena was so angry when she became Roman, becoming more of a demure goddess of crafts and cleverness, when they took away her military importance and the Greeks, nor Athena forgave them for that insult. Annabeth realizes that the Mark of Athena leads to a statue which the Romans took, and the children of Athena have been searching for it for centuries, starting civil wars. Aphrodite directs them to a map close by that was left by her siblings in 1861, and that Annabeth will face her worst fear.

Before Annabeth can reply, Hazel spots a pegasus pulling a chariot, and two giant eagles descending down to the dock. As they run back to the ship they are stopped by Octavian and two legionnaires. Annabeth chucks her dagger into the ocean, in a bid for Percy's help, Octavian is confused but orders the other two to lower their weapons. But Percy interrupts by flooding the dock and dragging the Romans into the sea, he tells Annabeth that she dropped her dagger. They run back to the Argo II and Annabeth and Percy pilot it to Fort Sumter. They see Frank as a giant bald eagle carrying Leo, and Jason riding the wind behind them, but Coach Hedge fires a 'warning shot' which knocks out the Roman chariot following them which then crashes into Jason and also singes Frank's wings so he drops Leo.

When Annabeth enters the fort she sees Leo firing at giant eagles, a full grown elephant who was rampaging around the flagpoles and Jason fighting Dakota before knocking him out. Fortunately there are a lot of tourists which cause chaos but also stop Annabeth from moving anywhere quickly. Annabeth gets shut in a room, only to see it swarmed by tiny black spiders. She panics and has a flashback, when she was little and spiders came at night, her step mother tells her to stop scaring her little brothers and she's only imagining it. The spider bites fade before she gets dressed and her step-mom thought that the cobwebs were a trick. On the third night, Annabeth ran away from home.

Gaea talks to her saying that although she would rather have Annabeth as a sacrifice, she will let the weaver take her revenge. Annabeth sees a red symbol of an owl blaze on the wall and the spiders disappear. She runs towards an old artillery piece that is glowing red, and using her knife retrieves a small bronze disc, which she stuffs in her backpack. She is confronted by Reyna, with her two metal greyhounds, when she tries to explain, Reyna cuts her off and tells her to come with her quietly, where she will be trialled and then painfully executed. Or Octavian will attack Camp Half-Blood, the location of which she told Reyna, Annabeth pleads that Reyna slow her down. Reyna says she respects her as they are both daughters of war goddesses, but she believes that Annabeth's quest is doomed to fail. Reyna retreats but swears that when they meet again, they will be enemies on the battle field. Annabeth runs for the ship and Piper pulls her onto the deck.