When Marco sees a news report about a downed nuclear submarine, he and the other Animorphs set out to find it in dolphin morphs. When the warheads in the submarine detonate, however, the group finds themselves transported through time by a Sario rip, to the era of dinosaurs (the Late Cretaceous period, to be exact). Rachel and Tobias are eaten by a kronosaurus and believed dead by the other Animorphs. The other Animorphs make their way to land, where they encounter a number of dinosaurs, including the Tyrannosaurus rex, which attempts to eat Jake. Jake morphs while inside the beast, injuring it and causing it to spit him out, and die but not before the other three Animorphs acquire it.

Tobias and Rachel, meanwhile had escaped from the kronosaurus, and make their own way to land. Tobias' wing has been broken and was unable to be healed by morphing, most likely as a result of the time travel. The two of them have a run-in with a pack of Deinonychus, but both manage to acquire the pack's leader and escape. Later they encountered by a vicious antlike alien race known as the Nesk, who attempt to kill Rachel and Tobias.

The six Animorphs find themselves reunited above a large canyon on a force field with an artificial city at its bottom. After investigating it, they are welcomed by an alien race known as the Mercora, who had fled their own planet which was destroyed and intend on making Earth their new home. However, they are at war with the Nesk, and do not have the technology to help the Animorphs return to their own time. The Nesk, however, do—so the Animorphs storm the Nesk's camp in order to steal a warhead to recreate the explosion that sent them into the past. The Nesk angrily flee Earth, but divert the path of a nearby comet towards the planet. The Mercora respectfully ask the Animorphs to surrender their warhead, thinking they can use it to dissolve the comet, and Tobias agrees to let them have it. However, realizing that the Mercora must have died in the explosion as they are not a current part of Earth and that the comet will cause the Cretaceous–Paleogene extinction event, he tells Ax to render it useless. The Animorphs escape back into the ocean, and the force of the comet propels them back to their own time. They are unable to use their dinosaur morphs following this book.

Jake -Bottlenose dolphin, peregrine falcon, Tyrannosaurus rex.

Rachel - Bottlenose dolphin, grizzly bear, Deinonychus, bald eagle, great horned owl.

Tobias - Bottlenose dolphin, human (himself), Deinonychus.

Cassie- Bottlenose dolphin, osprey, Tyrannosaurus rex, great horned owl.

Marco - Bottlenose dolphin, osprey, Tyrannosaurus rex.

Ax - Bottlenose dolphin, human (main), northern harrier, Tyrannosaurus rex.

The summary on the back cover is narrated by Rachel.

In the Time of Dinosaurs was published with seven different covers. The first six had the same front cover design, but in different colours, with one of the six Animorphs shown on the first-page illustration. Jake (purple) is shown half-morphed to jaguar, Rachel (green) is shown half-morphed to bear, Tobias (blue) is shown as a hawk, Cassie (blue) is shown half-morphed to wolf, Marco (red) is shown half-morphed to spider and Ax (yellow) is shown in his natural form. A seventh alternative had a multi-coloured front cover, with all six morphing pictures combined on the first-page illustration.

A promotional poster for Megamorphs #2 depicted Marco morphing into a Tyrannosaurus, Cassie morphing into a Parasaurolophus, Rachel morphing into a Styracosaurus, and Jake morphing into an Archaeopteryx. The latter three morphs were never depicted in the book.

In the Time of Dinosaurs is the only Megamorphs book that has a front-cover quote: "<No one knows who we are...>"

The dinosaurs that appear in the book actually existed in different areas and prehistoric eras, so K. A. Applegate added a note from Tobias, explaining that - within the context of the story - paleontologists are actually incorrect about these animals. The genera that appear in the book are Elasmosaurus, Kronosaurus, Saltasaurus, Tyrannosaurus rex, Hadrosaurus, Triceratops, Deinonychus, Spinosaurus, Pteranodon, and Iguanodon.

This is the first book to feature all the Animorphs, including Ax on the cover.