Thomas & Friends: The Revenge of Sailor John is the sequel to Thomas & Friends: Sodor's Legend of the Lost Treasure. This sequel is more darker toned than the special was
The game begins with a flashback to Sodor's Legend of the Lost Treasure with Sailor John trying to destroy Thomas with dynomite and getting arrested by the police. It then forwards to many years later, where Sailor John is starting a new plan, to destroy Thomas once and for all and to make himself the controller of Sodor. He then breaks out of jail with a crowbar he found and is set off for sodor.
The day in Sodor is a usual day of all, with Thomas shunting Gordon's express coaches and then himself is going onto his branch line with Annie and Clarabel. Thomas is feeling happy go lucky with himself that he is being really useful and he makes all the engines all feel happy go lucky as well.
Thomas' mood dampers when he is in for a shock: He notices a Newspaper on the platform that said in big letters "Evil Pirate escapes Jail, plans to take over Sodor and destroy Thomas". When Thomas returns to the shed the next day he tells the other engines about Sailor John escaping jail and the plot of him destroying Thomas himself. The engines plan to help Thomas save his life and the next day tell this all to The Fat Controller.
Thomas however was extremely paranoid about his life that he passes through a red signal and collides with Diesel at the points. Diesel was cross with Thomas about this but Thomas tells him about Sailor John's plot to destroy him. Diesel wasn't impressed with Thomas' plan but he would tell the other Diesels that they would help stop Sailor John, because without Thomas they wouldn't have rivalries. After both engines are rescued by Rocky and Edward they head off to the Dieselworks to talk about the plan to the other Diesels, who decided to agree. Whenever any of the diesels saw the nasty pirate, they would pretend to be friends with him.
Sailor John however has finally arrived on sodor, and had some dynamite in his hands and was ready to destroy Thomas once and for all. Diesel 10 noticed him and decided to assist with Sailor John, but what Sailor John didn't know was that Diesel 10 was just faking it, he was only pretending to be friends with Sailor John so he could stop him.
At the Dieselworks, the diesels were holding Thomas hostage (they were pretending though) as Diesel 10 heads up to Thomas. Sailor John was ready to blow Thomas up, but then Diesel 10 bumped Thomas where the dynamite flew into the sky rather than Thomas. Sailor John finds out that the Diesels tricked him, and now Sailor John had a brand new plan, rather than destroying simply Thomas, he would destroy everything on the island and make it his dream island just for himself and his stolen money.
The engines all chuff away as Sailor John holds a giant flamethrower on a powered truck, but luckily James bumps the truck that it derails and the flamethrower begins to explode, and then it does which the engines watch and think that killed Sailor John.
However it turns out he isn't dead, he is instead Giant, Angry and overall furious. He grabs Thomas with a rope, and brings him down and then kills him once and for all with a huge bomb. But 1 second into the bomb going off Sailor John accidently kicks it away along with himself and kills himself into the water.
Even then Sailor John stills survives the explosion and then finds Captain with the police, who take him away back to jail where he belongs, and Thomas is put back on the rails.The Fat Controller was cross about Sailor John destroying part of the island, but is very proud of Thomas and all his engines for stopping Sailor John's plot to take over the island.
The movie ends with a huge parade with Thomas as the leader to celebrate Sailor John's arrest, again.
After the credits Sailor John plans another revenge, but then finds out he has done quite enough and decides to remain in jail.