Thomas gets lost in the mountains and discovers an old town, and soon everyone hears about his discovery. He later grows jealous of a new tank engine named Stanley.
The Great Discovery contains examples of:
- Always Someone Better: Thomas in regarding to Stanley.
- Armor-Piercing Question: The Fat Controller furiously asks Thomas why did he shunt so many trucks for Stanley. Thomas doesn't respond, feeling ashamed of what he had done.
- Attention Whore: A big plot point in the special.
- Creative Closing Credits: The movie ends with a special edited version of "Engine Roll Call" to include Stanley, followed by the first proper soundtrack song "Thomas You're The Leader", set to a montage of scenes from the movie and past two seasons.
- Earn Your Happy Ending: For both Thomas and Stanley, the latter rescuing the former who makes up with him and they celebrate the grand opening of Great Waterton together.
- End of an Age: This is the final Thomas and Friends production in the live-action model era. The next season will have a hybrid of CGI animation and models, while the next special switches to full CGI.
- Grand Finale: Of the live-action model series of Thomas and Friends.
- Green-Eyed Monster: Thomas towards Stanley, but in the end, he becomes friends with him.
- Gone Horribly Right/ Nice Job Breaking It, Hero!: Thomas grows even more jealous of Stanley after he takes his place on the Great Waterton restoration project. He then decides to make Stanley look foolish by giving him a long freight train too heavy for him to pull. Unfortunately, the prank backfires as the coupling snaps and the trucks race down the hill, veering into a siding and crashing into the newly-built Great Waterton tower, and poor Thomas is left shunned.
- Heel Realization: After his prank on Stanley backfires horribly, Thomas immediately realises how low he sunk and says nothing to excuse his actions.
- The Movie: While not the first feature-length Direct to Video special from the franchise, it was the first to be advertised as this (instigated after Lionsgate purchased the home video rights to the series from Fox, who had advertised it as a "Full-Length Feature" in an early trailer for the film).
- Now, Let Me Carry You: Stanley rescues Thomas, but breaks down in the process. Thomas then helps Stanley back home, and the two become good friends ever since.
- Rhymes on a Dime: Thomas gets a few. One of them being, "I am brave and I am strong. I'll get to the wharf and it won't take long!"
- Shamed by a Mob: Thomas gets shunned by the others after giving Stanley too much trucks, which led to the Great Waterton tower to crash. James in particular makes clear he knows full well why he did it.
- Shout-Out: The plot of a character feeling threatened by a newcomer who everyone likes quickly calls to mind Toy Story.