Rachel's father asks her to move with him to another state. After some reconnaissance work, Marco and Tobias find an entrance to the underground Yeerk Pool, in one of the changing rooms at The Gap. The Animorphs decide to infiltrate the pool and to try to find the location of the Earth-based Kandrona by going in as cockroaches. Once inside the complex, however, they get caught on the tongue of a Taxxon. As they are about to be devoured, time freezes and they feel themselves being forcibly brought out of morph. They are rendered human once again, including Tobias. They are then introduced to an all-powerful being called an Ellimist. The Ellimist tells the kids that he cannot interfere with other species, but when species are in danger of becoming extinct, he can step in and save a sample. He informs them that he wants to preserve part of Earth's beauty, along with some humans, because the Yeerks are going to win the war in the future.

The Animorphs ask how much time they have to consider the offer, but the Ellimist tells them that they must decide now. If they choose yes, they and their families would be transported to another planet, but if they choose no, everything would be returned to the way it was before the Ellimist's arrival. The group puts the decision up to a vote, and during the deliberation, Jake and Rachel notice a drop shaft and a human frozen in the act of moving up in it. The Animorphs choose not to accept the Ellimist's offer and are immediately back in cockroach morph on a Taxxon's tongue. They are able to demorph and fight their way to the drop shaft to escape the Yeerk pool.

Later, the Ellimist appears to the group again to give them the choice one more time. To aid their decision, he transports them to a grim future in which the Yeerks have enslaved Earth, the Animorphs encountering the future Visser Three- now Visser One- and an infested Rachel (although it is hinted that this timeline is actually an alternate future rather than an actual future for the Animorphs' true timeline, as Rachel's Yeerk is confused by the presence of Ax and refers to six humans coming into the future, suggesting that she is from an alternate timeline where Ax was never rescued and/or another person was with the main Animorphs when they walked through the construction site). Rachel notices, with some confusion, that most of the skyscrapers and buildings in the city have been leveled except for the tallest one: the EGS Tower. This tower stood at the base of a large, open Yeerk pool and was covered with a shiny dome. After they return to their own time, the Animorphs reverse their earlier decision and accept the Ellimist's offer. They expect to be immediately whisked away, however, nothing happens.

Rachel is disconcerted by this and concludes that the Ellimist did not transport them because he wanted a different answer. While thinking on it, she realizes that only because of the Ellimist's first appearance were they able to see the drop shaft and know that there was a chance to escape the Taxxon's grip. She then determines that during the trip to the future, the Ellimist was once again simply trying to show them something that he could not overtly tell them without interfering. She remembers the EGS Tower, deduces that the Kandrona must be located there, and gathers the rest of the Animorphs for a raid.

After a vicious battle just before dawn, the Animorphs manage to take the top floor of the tower and destroy the Kandrona by shoving it out of the window. The Ellimist appears to them again, and confirms Rachel's suspicion that even he cannot tell the future, and humans might win the war yet. Rachel tells her father she can't move with him.

Jake -Cockroach, Siberian tiger.

Rachel -African elephant, great horned owl, cockroach, grizzly bear, bald eagle.

Cassie -Cockroach, wolf .

Marco -Cockroach, Silverback gorilla.

Ax -Human, cockroach.

The Ellimist is introduced.

The Earth-based Kandrona of the Animorphs' city area is destroyed, but it is replaced three weeks and a few books later.