WMG: Dinosaur Train

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!

Shiny has OCD
She also needs to have things her way, and was quite frustrated when her family doesn't let her.

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.

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.

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.

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.

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.