The Scientist is a fan fiction based on the television series Thomas the Tank Engine and Friends.
- Topham Hatt - A young apprentice at Swindon. Heartbroken by a tragedy, he sets about designing a locomotive that would have prevented it. But his naivete and brilliance may cause the destruction of everything he holds dear . . .
- Jane Brown - A girl Topham's age who is staying at Swindon while her father is on a business trip. She and Topham become friends, and is the first to find out about Topham's "experiment".
- Diesel 10 - A locomotive built by Topham, with an experimental claw. He is devoted to his builder, but when Topham turns his back on him, he rebels . . .
- Jenny - A good-natured old "Dukedog" locomotive, and a goods engine. Topham often works with her.
- Elizabeth - An old -er, vintage- steam lorry who works at Swindon.
- Nate Winston - The supervisor's nephew; he attempts to make life miserable for Topham.
- Mr. Winston - The supervisor. He oversees Topham's education.
- Harry - Mr. Winston's private locomotive. Like his owner, he's strict, but kind.
- Max - A cheeky little pannier tank engine.
- Isambard - Nate's locomotive; he is devious and deceitful.
- Thomas - Topham's old friend, an L&YR class 21 tank engine.
Topham is sent by his father to be apprenticed at Swindon locomotive works, under his friend Mr. Winston. Taking his best friend Thomas the class 21 with him, he soon learns his way around the workshop. He makes friends with Jenny, an old freight engine, and Elizabeth, a crotchety steam lorry. Mr. Winston's nephew, Nate, sets out to make his life miserable. Topham also meets and befriends Jane Brown, daughter of the Skarloey Railway's manager.
Tragedy strikes as a fire destroys the engine shed. Most of the engines make it out, but Thomas' path is blocked by debris and cannot be saved. Topham, maddened by grief, starts building an engine with a claw that would have saved Thomas.
Topham builds his engine in a large, abandoned engine hangar. He scrounges together the parts necessary for the engine. With Jane's help, he begins construction. To protect his hair, he dons an old, battered top hat, which is far too big for him.
When the engine needs a name, Topham takes an old nameplate reading "Diesel 10". He christens his engine Thomas- after his old friend.
Thomas is almost complete. But meanwhile, Nate has noticed Topham's strange behavior and alerts his uncle. Topham and Jane escape the hangar, but Thomas is found and sent off to the scrapyard.
Topham finds Thomas and finishes wiring his electronics so he can get away, although his claw is not operational. But, the next morning, he discovers that his friend Max has been badly damaged during Thomas' escape. Disgusted, he disables Thomas' circuitry completely and throws away his hat.
Nate finds Thomas, and foolishly reactivates all of systems- including his claw. In return, Thomas picks him up and flings him aside with his claw, badly maiming his leg. Topham finds him and helps him to the hospital, beginning a friendship between the two. Thomas is unheard from for some time.
One night, it is discovered that the express has been commandeered by a rouge diesel engine. Topham knows he must finish it with Diesel 10. Working with his friends, he creates a plan. Just before he leaves, he dons his hat once more. This time, it fits.
Jenny and Nate send Jenny behind the express, couple up, and apply the brake. Meanwhile, Topham drives Elizabeth parallel to the train. He jumps onto Thomas' sideplates, just dodging his claw. After nearly perishing by Thomas' claw, he applies the emergency brakes, and collapses from exhaustion and injuries.
Waking up a few days later, he learns the train stopped a few feet from the buffers, and everyone is safe. He limps down to the statoin to see Thomas -his claw deactivated but not removed- as he is shipped away to shunt at a large yard. He notices that his nameplate has fallen off, and throws it away, telling Diesel 10 that he doesn't deserve a name.
He watches as Diesel 10 rolls away intot he horizon.