This book loosely follows the plots of Animorphs books #1: The Invasion, and #11: The Forgotten. The book narrates from the reader's point of view, as a sixth Animorph, and they are able to choose their morphs as the story progresses.

The book opens up with the reader ("You") riding their bike around the abandoned construction site. They join up with the Animorphs, witness Elfangor's demise at the hands of Visser Three, and pedal furiously home. The next morning, Marco comes to the reader's house to explain that they have all started acquiring morphs, and that they plan to investigate a Sharing meeting that evening. A correct choice by the reader of a ferret as their first morph leads to Ms. Humphries, the reader's next-door neighbor with a lot of ferrets and cats. Ms. Humphries is a controller and takes several ferrets (including the reader in morph) to a meeting of The Sharing. She puts the reader down near a volleyball net, and the reader calls to Cassie for help. Cassie lets them escape and demorph with only a few minutes to spare. The reader suggests acquiring better morphs than just lizards, dogs, cats, and ferrets, and Rachel agrees and Cassie leads everyone to The Gardens.

The gang split up when a security guard with a golf cart chases them, and they find themselves inside the giraffe exhibit. The reader acquires the giraffe, then re-enters the hallway. After two animal handlers leave a tranquilized female hyena, they enter and acquire her DNA. As the reader leaves, they are caught and detained by park security. The reader morphs Princie, one of their dogs, and leads the team astray by not following their (human) scent, leading them to Ms. Humphries' house, and rubbing their sweatshirt (left outside earlier) over everything in the neighborhood before running home.

Knowing that the reader has to meet up with the rest of the Animorphs in their trip to the Yeerk Pool, they decide on a morph to sneak in with. A failed choice of the K9 police dog leads to the reader being recognized by Finley, the taller police officer. After the Animorphs battle and escape from the Yeerk Pool, Visser Three kills them with his eight-headed, fireball-launching alien morph.

A correct choice of a ferret morph has the reader hiding in the elevator leading down to the Yeerk Pool, one of many entrances. Some people take notice of the reader, and are about to get rid of them, when Jake's brother Tom spots the reader and recognizes him as one of Ms. Humphries' pets. He says they shouldn't touch "it", because "Chapman said to take no chances."

At the bottom floor, another Controller presses a series of buttons on the elevator, making it go past where normal people should be able to get to. The elevator opens up, and the reader discretely follows the Controllers down a staircase to the giant cavern that holds the city's main Yeerk Pool. They see multiple hosts (human and Hork-Bajir) in cages, a woman re-infested, and Tom being put into a cage. The reader also sees Cassie about to be led to the loading pier.

Running in her direction, Tobias spots the reader and they tell him that they all have to save Cassie. Then the reader runs to Jake, Rachel, and Marco, who haven't morphed yet, and Jake tells them to demorph behind a storage shed. Rachel tells the reader to rest and wait for them. A few minutes later, a male human-Controller, a Hork-Bajir, and Taxxon find the reader. Rachel, morphed as an elephant, rescues the reader, and they all run to save Cassie. The reader morphs into the hyena and kills a Taxxon. Marco is a gorilla, Jake is a tiger, and Rachel is still an elephant.

Events transpire much as they did in The Invasion, with Marco unlocking cages, Cassie being rescued and morphing into a horse, and Visser Three entering the scene. He morphs into a giant eight-headed, eight-armed, and eight-legged creature that breathes fireballs, and Tom tries to attack the Visser. The gang escape into the school hallway, run outside, and demorph.

A few months later, Ax has joined the group, and the reader is in their kitchen at home when they start having flashing visions of being in a jungle. The reader rides their bike to Jake's house and tells him what's happening. He remembers the events of Book 11, but even though the rest of the Animorphs were there too, they don't remember it. Now it's the reader's turn to be having the flashes instead of Jake. Suddenly, the Sario Rip flash takes the reader and Jake into the rain forest, and Jake distinctly remembers being there in The Forgotten. He leads the reader to a downed Bug fighter, saying that they have to take the onboard navigating computer before Visser Three comes back. Cassie recalls being on the Bug fighter shooting Dracon beams at Visser Three's blade ship, and Jake notes that the last time a Sario Rip happened, he had to die and he doesn't want to do that again.

Ax and Jake decide that this second go-around means that they should do things differently. Jake decides to have Ax disable the computer instead of taking it, to make it look like it happened in the crash. The gang decide to morph parrots and fly through the jungle. The reader see human- and Hork-Bajir-Controllers destroying the rain forest, and Polo's tribe spying on the Hork-Bajir. They land on their shoulders, and Cassie demorphs first. She reveals her human head and retracts her bird tail first, to give the appearance of being an animal spirit. She communicates with the small tribe by way of dirt drawings. Through these drawings, she conveys that the Hork-Bajir (diablos) are the enemy to be fought, and that she and her (bird) friends need to get on board the Blade Ship with the tribe's help. She arranges to meet up with the tribe again just before dusk.

As chameleons, the gang make their way to the Blade Ship. When the reader sneaks on, Ax suggests the reader split up to avoid attention. After some brief arguing over whether the gang should kill Visser Three in "this timeline" and what it might mean, Visser Three boards and orders both the Blade Ship and the fixed Bug fighter to start up. Both ships rise, and before the gang can attack, the ships fire at each other, closing the Sario Rip when the Dracon beams intersect. The reader is suddenly back in their hometown (as a human), albeit a year too early.

The reader is at a bus stop with Rachel and Marco. Suddenly, Marco's mom drives up to the curb, and she offers Marco a ride home. The reader and Marco are shocked at this because (at least in the proper timeline), Marco's mom is "dead" - rather, the host of Visser One. Suddenly, Visser Three comes running to attack Eva as a Pit Bull. The reader morphs into a giraffe to attack the Visser. The second the reader kicks him, they are suddenly back in their own home in the kitchen. The reader runs over to Jake's house, where he and Ax are eating licorice sticks and pizza like they were when the reader first ran over there before the Sario Rip.

Ax and Jake figure out that Visser Three had tried to use a Sario Rip to his advantage to go back in time and kill what would be his rival's human host. They go into a detailed explanation of exactly what transpired in the Sario Rip and why certain individuals remember what they remember, or why they did what they did. Jake concludes by saying that it's good that they've restored the correct timeline, and that "there will still be more battles to fight." The reader adds "But first, there's pizza." This is the winning ending.

A hidden message, reading <JOIN US>, can be found on the book's cover.

The cover reads "You are the sixth Animorph," but there are seven Animorphs on the cover. This is because the editors never referred to Ax as an Animorph, but to be what the Yeerks call him - an Andalite bandit.

The you in this book is not the same you from #2.

The Alternamorphs were a spin-off series that had no actual effect on the continuity of the storylines in the Animorphs books. These books were taken from the same idea as the Goosebumps: Choose-Your-Own-Adventure books. They put you (the reader) into the perspective as the new Animorph who joins the team. At the end of each chapter, you are given 2-3 choices, with each choice leading to a different scenario, and ultimately a different outcome.