The Flynn-Fletcher family goes for a trip to the local museum, and while the parents are enamored by the dinosaur exhibit, Phineas and Ferb find themselves excited by the “Gadgets Through the Ages” section. Finding an old time-machine, the boys decide to repair it; but everything goes wrong when they get themselves and Candace trapped in the cretaceous period. Somehow, they need to get a message back to the present, so Isabella and the Fireside girls can come rescue them!
Perry, meanwhile, is dealing with a personal crisis… coming into Doofenshmirtz’s lair that day, he hears the incriminating sound of fighting, and a paw print on his cheek. It turns out that the doctor has been fighting another nemesis, Peter the Panda, behind Perry’s back! Deeply hurt, Agent P discovers that without someone to stop, his life just isn’t quite the same- and even Doof finds himself missing his monotreme.
- Batman Gambit: Doofenshmirtz was only pretending to dump Perry, to ultimately get as many secret agents together as he could, to take them all out.
- Does This Remind You of Anything?: Perry getting replaced as Doofenshmirtz's nemesis is played like a breakup, and Peter getting treated like a homewrecker. They even got on a talk show with Peter getting booed by the audience.
- Get Back to the Future: After their time machine is broken.
- Lost Love Montage: Perry, thinking of the times he fought Doofenshmirtz.
- Pandaing to the Audience: Perry's apparent replacement is a panda.
- Ripple Effect Indicator: Mud fossils keep getting changed as the mud in the past is altered.
- Time Machine: That looks just like the device in The Time Machine.
- Write Back to the Future: Only Phineas misspells "time" as "tie", causing the Fireside girls to make the wrong machine at first.