Phineas and Ferb repair a broken time machine from the museum, and they then travel back in time, accidentally taking Candace with them. The Fireside Girls build a replacement machine to rescue them. Meanwhile, Doofenshmirtz replaces Perry with a new nemesis named Peter the Panda, making Perry depressed.
Phineas and Ferb visit the Danville Museum. Dad finds a dog skeleton, that was found in their neighborhood. Phineas notices the collar saying "Bucky" and comments "Didn't we have a dog named Bucky who got sick and went to live on Kindly Old Man Simmons's farm?" Dad continues on and finds a human skeleton. "And this here is Kindly Old Man Simmons- Hey, who's up for milkshakes?"
Ferb taps Phineas on the shoulder and points to an exhibit. Phineas' eyes immediately fall on a sign that says "Gadgets Through the Ages." They enter the exhibit and find a tour guide talking to several people about a time machine that was never finished. Phineas realizes that he wants to fix the time machine, and exclaims that he knows what they're going to do today. He then asks where Perry went. Agent P enters his HQ through a photo booth. He sees Major Monogram frozen on the screen (from being shot by the Freeze-Inator). Carl than comes on and tells Perry to stop Doofenshmirtz. Candace sees Phineas and Ferb fixing the time machine and takes a part from the time machine that plays a major role in going back in time. Phineas puts two wires together and Candace runs off with the piece for the second time.
Candace meets a boy outside the museum that stole a Pterodactyl. He decides to help her and creates a diversion by yelling. All the security guards are attracted to him and Candace sneaks inside the museum. She sees Jeremy and goes to talk to him. He tells her that he is so bored that by the time his job finishes, he'll be part of the fossil exhibit. Candace laughs and spots a security guard entering the hall, she then runs off. Meanwhile, Perry meets Doofenshmirtz at his building but sees Doofenshmirtz's silhouette in the window. His silhouette shows that he is fighting with an evil ray gun. Perry enters and Doofenshmirtz seems to be trying to hide something. Perry then goes over to a closet that's shaken and see Peter the Panda in it. Doofenshmirtz then tries to deny knowing Peter.
Phineas and Ferb are testing their time machine. Phineas tests number 1. Candace is just calling for her mom and she gets teleported back to when she laughed at Jeremy's joke. Jeremy asks Candace where she ran off to, but Phineas tests number 2. Candace says, "That's a good one!" as she rewinds back in time. Jeremy laughs in a kind of confused way as Phineas tries out number three. Candace laughs and says, "Hi Jeremy!" Jeremy starts to get freaked out. The security guard then asks if Phineas and Ferb need anything after finding them fixing the time machine. Phineas asks for the piece Candace ran off with, and the security guard says he'll keep his eye out for it. Back at Doof's place, Doofenshmirtz states that they met at an evil convention and they immediately disliked each other. He says that he just wants a clean break, and Perry exits the building to "When We Didn't Get Along", feeling heartbroken because his only nemesis has left him for another one.
Phineas test number 4 and Candace gets transported right in front of the security guard. The security guard takes the piece away just as Phineas test Number 5. The security guard asks if the boys need anything again. Phineas, a little confused, asks for the piece again. The security guard comes over holding the piece in his hand and hands them it. The boys then complete the time machine. Lawrence asks for money for the audio tour and Candace tries to drag Linda over to the exhibit where Phineas and Ferb are fixing the time machine. When Linda steps through the hall, Candace strays over to Phineas and Ferb right when they are testing the time machine. They go back in time to 300 million B.C. where a T-rex steps directly on the time machine, smashing it.
Phineas, Ferb, and Candace encounter the T-Rex, and Phineas and Ferb do not make any sudden movements. Candace, on the other hand, makes many arm movements and screams, causing the T-Rex to chase after her. Phineas and Ferb use a scooter and chase after Candace (while wearing turtle helmets). Candace falls in the mud right where the footprint from the museum ends up being. Lawrence tries to show Linda, but the boys' fun over the Candace print with their scooter. The three then escapes the T-Rex from hanging onto leaves and vines in an herbivores mouth. They then walk back to the mud puddle and they realize the T-Rex footprint is the same footprint in the museum that Isabella and the Fireside Girls are currently looking at today. They write a message to Isabella, saying that they are stuck in 300 million BC and for them to build another Time Machine to save them. Isabella does what they ask but Phineas misspells Time Machine, making it say "Tie Machine" (but the real reason the machine didn't work was that they didn't have the piece that kept teleporting Candace everywhere. Isabella takes matters into her own hands and constructs a real Time Machine and they are saved.
Back at Doofenshmirtz's place, Peter and Doof are fighting and rip a picture of Doof. Doofenshmirtz than has a flashback to "My Nemesis". Peter takes his chance and dismantles the Freeze-Inator. Perry and Doofenshmirtz attend Dr. Feelbetter's show, where all the secret agents are gathered in one room. Doof than feels guilty and asks for Perry to be his nemesis again and Perry accepts. He then traps all the agents in their chairs and says he'll use his real Freeze-Inator to freeze the agents for his giant chess set. Perry, however, gets the remote for the chairs and the agents take down all the evil scientists.
Isabella travels back and saves the trio, but the Time Machine needs to be plugged in. A bolt of lightning hots Candace while she's holding the plug. Everyone comes back to the present, but the T-Rex comes too and starts to chase Candace again. The Freeze-Inator blasts out the ceiling of the building and hits the T-Rex in the museum right when Candace is about to show her parents the dinosaur. Phineas and Ferb were happy with what they did today in the museum. As they leave, Candace was blushing when Jeremy pointed out that his favorite was the "C + J heart" sign that she drew back in time. Then Jeremy wonders why cavemen were wearing turtles as safety helmets.
That night, Linda is asleep in bed until Lawrence wakes her by replaying Fossils...da da da over and over again on the recorded tape. Linda gives him a little grin.
- Vincent Martella as Phineas
- Ashley Tisdale as Candace
- Thomas Sangster as Ferb
- Caroline Rhea as Mom
- Alyson Stoner as Isabella
- Mitchel Musso as Jeremy
- Dan Povenmire as Dr. Doofenshmirtz
- Richard O'Brien as Dad
- Dee Bradley Baker as Perry, T-Rex
- Tyler Mann as Carl
- Tiffany Espensen as Ginger
- Isabella Acres as Katie
- Carlos Alazraqui as Dr. Feelbetter
- The motor scooter's track disappears while Phineas and Candace talk about the footprint.
- Peter the Panda threw all the chairs in the left entrance, but when Doofenshmirtz made some guys enter with the Freeze-inator, they entered from the left entrance and the chairs were gone.
- When Dr. Doofenshmirtz is showing Agent P to the door, Agent P's height is just under the doorknob, but when Dr. Doofenshmirtz is closing the door, Agent P grows to be half the height of the door.
- As Perry leaves Dr. Doofenshmirtz's room, he hears him say "Curse you, Peter the Panda!" which most likely means that Peter the Panda had destroyed the Freeze-inator Ray, however, later in the episode Peter the Panda is seen disassembling the Freeze-inator. Doofenshmirtz may have said this to make Perry sad.
- The T-Rex smashes Phineas' motor scooter along with the time-machine, yet the boys ride on it in perfect condition to save Candace. Later they drop it in the water, but Ferb is seen wheeling it along soon after.
- During the Doctor Feelbetter show, Doofenshmirtz recognizes Perry, although he is not wearing his hat.
- When Isabella and the Fireside Girls read the message in the fossilized footprint, Holly doesn't wear a beret, and then after Isabella finishes reading it, Holly is now wearing her beret. Also, Gretchen's skin color continues into the bottom half of her glasses frame in this same scene.
- Carl doesn't have the '3' inside his ear when he first appears.
- After Dr. Doofenshmirtz finishes singing he sees Peter the Panda taking apart the Freeze-inator Ray. There are some parts of the Ray sitting on the ground, but when the next scene comes the parts are gone.
- When Peter the Panda breaks Dr. Doofenshmirtz's picture, Doofenshmirtz is holding it upside down, but in the next scene, it is shown right side up.
- While Katie was hammering the time machine, her collar is orange instead of red.
- When the T-Rex is shown in the rain if you look closely Candace's drawing is gone.
- Right before she gets stuck, when Candace is complaining over the fact that there is no electricity, her lips are out of sync from what she's saying.
- When Candace gets struck by lighting there's a space between Katie and Adyson in the time machine, but when they travel back to the Danville Museum there's no space.
- When Isabella was telling Phineas that there is an 'm' in 'time machine', the whites of Gretchen's eyes can be seen.
- T-Rex's have two fingers, but the one in the episode is seen with three, which is a very common mistake in many shows.
- When Isabella first read the message on the stone, there was an 'm' in the word 'time machine' when she read it. Although, she may have made a mistake or she didn't read it well.
- During the song "When We Didn't Get Along", Perry puts his hat into the nook in the wall, but on Doctor Feelbetter's show when Doofenshmirtz begs to be forgiven, he pulls it out of nowhere.
- When Phineas says, "It occurs", Phineas' shirt only has two stripes. Usually, it has three stripes.
- In reality, there were no cavemen during the day when the dinosaurs lived. However, in the end before the ending credits, Jeremy said, "Hmmm. I never knew cavemen wear helmets before." when actually there is still no cavemen before.
- The Closed Captions spelled Doofenshmirtz's name as "Doofashmirtz".
- Dinosaurs did not live in 300 million BC, which was during the Carboniferous Era. In fact, the first dinosaurs appeared 50 million years later.
- When Monogram first appears, his shirt sleeve is missing its dark green stripe and only appears after Carl knocks him over.
- During "My Nemesis," at one point the tambourine becomes transparent.
- The end credits has Lawrence in bed, listening over and over the ending of the audio tour.
- This is the first two-part episode.
- Major Monogram did not speak in this episode, possibly due to him being frozen by the Freeze-inator. However, he does grumble when Carl attempts to make a conversation with him.
- The Time machine is invented by Professor Onassis is seen in the episode "Phineas and Ferb's Quantum Boogaloo".
- On the talk-show, Doofenshmirtz breaks the fourth wall by saying, "cartoonish physical violence".
- Agents D, F, R, C, O, K, H, and the unnamed kangaroo from "Traffic Cam Caper", can be seen in Dr. Feelbetter's studio.
- The time machine is based on H. G. Wells' famous novel The Time Machine.
- During the "My Nemesis" musical number, caricatures of The Archies, a fictional garage band in the animated television series The Archie Show, are shown and begin to sing and play instruments during the course of the sequence. The song itself parodies the style of musician Elvis Costello.
- The Dr. Feelbetter show is a parody of confrontational talk shows Dr. Phil and The Jerry Springer Show.
- The episode has several references to Jurassic Park, particularly the role of the Tyrannosaurus Rex and destroying the time machine being similar to the scene when the T-Rex destroys the jeep. Also, when Phineas tells everyone not to move, Candace flips out, like a scene from Jurassic Park III. Finally, when Candace is trying to stop her parents from going into the exhibit, we see the T-Rex blinking its eye as from the movie.
- When the message appears on the dinosaur footprint, it fades into existence just like when the future changes in each of the Back to the Future movies.
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