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The asteroid that wiped out the dinosaurs wasn't an accident
The series takes place on earth, which means it must follow the laws of physics. This means that with a time machine, the furthest back you can travel with a time machine is to the moment it was turned on. We see the kids meet early dinosaurs and crocodiles, so that means that dinosaurs have had time travel throughout the Mesozoic Era, so they had the technology for 100 million+ years. We also see that aside from trains they have submarines and zeppelins, so what if they developed space travel too?

What if the asteroid dropping on earth was the last act in a war between the dinosaurs and some other alien race?

Don has Downs Syndrome

That's not an underbite, he's eating his own beak. He also asks questions that were just answered.

  • How would him eating his beak be related to down syndrome? Also, his asking a question that was just answered, he could just be asking to make sure his thinking is correct or that he heard correctly.
    • You're expecting logic on a wild mass guess? Okay, I'll give you a little: one physical sign of Downs is a flatter face. How do you do that with a long beaked/muzzled species?
      • Then so does Grandpa Pterodon has it too since the grandparents comment that Don has his grandpa's beak. Though Grandpa doesn't demonstrate many other signs of Downs.
      • How on Earth can something eat its own beak? It's a beak!
  • Don's behavior is closer to that of autism. In fact …

Don has autism
He loves collecting and a focus on a very specific topic (holes). Plus, he has a non-neurotypical way of looking at things.

Shiny has OCD
She also needs to have things her way, and was quite frustrated when her family doesn't let her.
  • She doesn't exhibit any signs of OCD. She just seems to be a bit of a perfectionist.
The Conductor is a Time Lord and the Dinosaur Train is his TARDIS.
He just uses the time tunnels to confuse the passengers, who completely unaware of the fact.
  • To take this one step further (don’t take this seriously at all, this is just me going insane), what if he’s the Doctor and Thurston is the Master? They mention going to school together, they’re friendly enemies, Thurston has the suave attitude of the Classic Masters and at one point they look like they’re about to re-enact Survival!

One of the stops on the Dinosaur Train's route is Milliways

Dinosaurs can travel through time whenever they get the urge, with nothing more than an easily obtained ticket. This is, of course, impossible. They can travel to pretty much any place on land and even under the sea using nothing more than a train. This is, of course, impossible. Not only that, but they can zip to those places in the space of minutes and be back home in time for supper. This is, of course, impossible. They can do all this apparently without any worries about being trapped in another time period or causing paradoxes. This is, of course, impossible. They can travel as much as they want and be sure of never meeting themselves because of the embarrassment this usually causes. This, even if the rest were true, is patently impossible. They can gather together dinosaurs of any species from any age together on a moment's notice without any adverse affects on the timeline. This is not merely impossible, but clearly insane, so after they've finished all of this, it only makes sense that they would round it off with a bite to eat at Milliway's, The Restaurant at the End of the Universe.

Humans created the Dinosaur Train, but the Troodons took it over
Some future inventors built a ring-shaped time travel device and put it in a truck trailer to accommodate its large engine, but traveled to the Civil War and eventually they ran out of fuel. So the inventors attached it to a steam train and plugged the engines together. However they were stuck again when the train ran out of fuel in the dinosaur times at what is now Troodon Town. The inventors were out of ideas until they saw two large rocks. They decided to tie one rock to the train and hit it against the other rock. After this, the inventors inserted the time machine and tested their invention out. After the test was successful, the inventors built some mind control helmets and enslaved the Troodons and taught them to speak English. The Troodon built a train line and the inventors marketed the train as the Dinosaur Train and created stations. However, the Troodon revolted, eliminating the humans, taking over the Train, and teaching other animals to talk. Eventually, the dinosaurs forgot about humans and lived in peace.
  • The episode "Back In Time" seems to support the idea that the time tunnels were not of dinosaur origin, with the revelation that some of them are, in fact, abandoned and unexplored.

Doc Brown and Captain Neweyes invented the Dinosaur Train
At the end of Back to the Future Part 3, Doc invented a train that can travel through time. Before the beginning of We're Back: A Dinosaur's Story, Captain Neweyes had invented a cereal that makes dinosaurs smart enough to think and talk. Maybe Doc ended up in the Mesozoic Era while on a "field trip" with his sons Jules and Verne, and the train lost the ability to fly. Then Neweyes (possibly one of Doc's sons) showed up, met Doc, and fed the local inhabitants, who happened to be Troodon, some of his cereal, making them smart enough to help make tracks for the train. In exchange for the Troodons' help, a special train was made just for them to use, and special tunnels were created with special tracks to boost the train's speed to 88 mph in order to time travel. The scientists got promises from the Troodon that the Dinosaur Train would never be used to travel to any time outside the Mezazoic. Then the Troodons took a bunch of Neweyes' cereal with them to every other time and place in the Mesozoic and fed every creature they found some of the cereal, whether dino, bird, reptile, or amphibian. The smartness created by the cereal was passed down to the offspring, and so on. The Conductor is from a long line of Troodon reaching back to the very first Troodon to eat the cereal.

Whoever/whatever created the Train and the Time Tunnels also created. . .
The Magic School Bus. Hey, somebody had to say it.

Buddy is a brood parasite
A mother Tyrannosaurus laid her egg in a Pteranodon nest the way a cuckoo lays it eggs in the nests of red warblers. Eventually, instinct will kick in and Buddy will eat his host family.
  • Jossed: Mrs Pteranodon mentions to Doris Tyrannosaurus in “I’m a Tyrannosaurus” that they adopted Buddy and just didn’t know which species he’d hatch into

The Conductor knows VERY WELL what lies beyond the late Cretaceous.
He's had regular nightmares about the asteroid ever since he saw it and its effects while mapping his routes, and is determined to keep the rest of dinosaurkind from learning about it for fear of causing a mass existential crisis; if someone ever asks for passage close to or past that time, he voids their ticket and firmly asks them to leave.
  • If he knows anything about the asteroid, he's a very good actor because in "Zeppelin: Crater," he and the other characters discuss the idea of an asteroid hitting Earth and he says that his mother told him that it's very rare and not something to worry about.

The show will get Darker and Edgier...
...but it is entirely possible that only slightly, and most darkness will be around the fact that there are unused time tunnels, and, of course, the Cretaceous Period.

The Time Tunnels connect to the Fraggle Rock cave system.
The caves of Fraggle Rock seem to occupy their own dimension, able to link to multiple worlds, and in one episode the charcters are sent back in time (although that seemed to be a one-off magical incident). It's theoretically possible that the caves could tunnel through time as well as space.

Additionally, the Fraggles appear to be some kind of small feathered theropod...

the Dinosaurs already know about the KT boundary event.

This guess is based on Isaac Asimov's The End of Eternity and the Star Trek episode All Our Yesterdays. The dinosaurs, having elected to develop time travel technology over space technology, have created a 200 million year eco technic utopian society that ends at the KT boundary. Dinosaurs living close to the boundary simply move backward when the end date approaches. It may be that the dead are buried near the boundary. This is no longer our world. If humans evolve post asteroid, the fossil record they see will be radically different from what we see. Perhaps one day those ape descended critters will find time travel technology and stop by for a visit.

Time travel itself funds Dinosaur Train Industries.

Dinosaur Train Industries is often coming out with new innovations such as a Dinosaur Train submarine, Dinosaur Train zeppelin, or a train that bores into the Earth's crust. They seem to have unlimited funding, and you can bet they're getting it from time travel to some rich source we're never going to be allowed to see.

Mrs Pteranodon is a abusive racist who's trying to get rid of Buddy, because he's not the same species as them.

Mrs. Pteranodon is abusive to her family and is racist towards Buddy when not on camera. She's discrete about it as to not get alienated by the rest of the dinosaurs and get banned from the Dinosaur Train. This is probably why they're going through to meet all the species: She's trying to find Buddy's family so that they can put him 'where he belongs' and 'live in peace'. However, the rest of the family know better, and probably won't let her give up Buddy. Mr. Pteranodon stays with her because he's worried Mrs will kill him if he leaves, and the kids because the Cretaceous doesn't have CPS.

Buddy is Sid's fursona.

Think about it. They basically have the same design except Buddy's an anthro dinosaur. Same eye shape, proportions, and general art style. Their designs are even both orange with blue highlights. They're both focused on hypotheses, research, and general science, and given Sid's age, him being interested in dinosaurs would be completely in character. The whole of Dinosaur Train is Sid and possibly his friends getting really invested in a combination roleplay/unit study on dinosaurs. Inaccuracies, and the time-traveling train, are due to the dinosaurs all being kids', albeit science-minded kids', perceptions, and them needing an excuse to explore creatures from different time periods. Dr. Scott the Paleontologist is a teacher trying to get the kids back on track and focused on real dinosaurs as opposed to fictional ones.

The asteroid never hit, and never will
Thus, dinosaurs remained the dominant species and evolved into the species that we see on the show.

The dinosaurs use Cenozoic mammals for their food
It would explain why the train has never gone forwards in time from the end of the Mesozoic as there’s nothing there but farm animals, essentially.
  • This opens up its own brand of Fridge Horror. As Cenozoic mammals ourselves, are we being farmed as a food source by hyper-intelligent time-traveling dinosaurs while being purposely kept in the dark about it? Is our entire civilization engineered for the primary purpose of feeding theirs? Dear god...
  • In the episode Father's Day, it is revealed that Mr. Conductor's father used his drill train to go to the Cenozoic but his train broke down and the tunnel collapsed, trapping him until the episode, in which Mr. Conductor uses a new drill train to go to the Cenozoic (who only knew the name of the era because the train Systems said so), and they get his father back to the Mesozoic.

Morris Stegosaurus is the reincarnation of Dion Dimetrodon
While there's no way they're biologically related, their personalities are too similar to be a coincidence.

This show is actually just a kid playing with their toys
Similar to The LEGO Movie, this show's events were actually created by a child with train and dinosaur toys. This explains all of the confusing time travel logic within the show. It helps that Craig Bartlett got the idea to make this show after seeing his son play with dinosaur and train toys.

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