Blue Mountain Mystery is the sixth Thomas movie. It serves as the Season 16 CGI Special.
It is a busy day at the Blue Mountain Quarry and as Paxton is pulling away from Owen with his loaded trucks, the keystone from Blondin Bridge comes tumbling down from above. Rheneas is traveling towards the crumbling bridge with his heavy slate trucks which push him onto the bridge. Rheneas just manages to clear the bridge before it gives way. Rheneas thunders down the line at high speed, knocking into walls on his way. When he comes to a stop, he is badly scratched, but not hurt. Paxton on the other hand has not been so lucky and has been derailed by rubble from the bridge. He is in need of urgent repair.
On Thomas' Branch Line, Thomas is working with Annie and Clarabel when a small red car lurches around the bend carrying the Fat Controller. Thomas is surprised, but the Fat Controller explains that it is Winston, his new track inspection vehicle. The Fat Controller tells Thomas that Paxton has been involved in an accident and that he is to take Paxton's place working at the Blue Mountain Quarry.
Thomas hurries to the quarry and spends the day working hard with his narrow gauge friends. When evening arrives, Thomas takes his trucks to Brendam Docks and returns to Tidmouth Sheds for the night. The next morning, Thomas is shunting trucks in the quarry when a mysterious green engine darts from a tunnel. Thomas introduces himself, but the little green engines does not reply and quickly rattles into another tunnel. Thomas asks Sir Handel who the green engine is, but Sir Handel tells Thomas he must have mistaken it for a runaway truck and hurries away. Then Thomas sees the green engine pulling slate cars. He asks Rheneas who he is, but Rheneas says that he does not know. Later on, Thomas sees the little green engine emerge from behind a shed. Thomas calls out to him, but the engine races away. Thomas decides to ask Rusty about the green engine, but the he hastily tells Thomas that it must have been a mountain goat and he rolls quickly away. Thomas makes his way to Skarloey, in hope that he will be able to tell him about the green engine. Just then, the little engine reappears and screeches to a halt. The little engine freezes and stares at Thomas before reversing into a tunnel. Thomas chases the little green engine all around the quarry, but the little engine is just too quick for him.
Soon Rheneas puffs along the line, accidentally blocking the little engine's path back to the tunnel. Rheneas apologises to the engine. Thomas overhears and realises that the others knew about the green engine all the time. Thomas later confronts Skarloey and asks him who Luke is, why he keeps puffing away, and why none of the others will talk about him. Skarloey decides that since Thomas is a friend, he can be let in on the secret. Skarloey tells Thomas that long ago Luke did something very bad and he thinks if anyone finds him, he will be sent away from Sodor forever.
That night, Thomas asks his friends at Tidmouth Sheds what the worst thing an engine could do is. The engines think hard and Percy remembers the time when he tried to sneak up on the coaches, but ran into a baggage trolley and covered himself and the Fat Controller in jam. Henry thinks of the time that he did not want his paint to be spoilt and stayed in the tunnel, only to be bricked up inside. Thomas recalls the time he ignored a danger sign and fell down a mine. James mentions the time Diesel pushed the trucks into the sea. But they all agree that none of that was bad enough to be sent away from Sodor.
The next morning, Blue Mountain Quarry is very busy. Rocky is moving stones from Blondin Bridge. Thomas wheeshes in to find Rheneas complaining to Skarloey about needing a new coat of paint after his accident. Thomas tells Skarloey that he has asked his friends and they have all decided that nothing is bad enough for an engine to be sent away forever. Skarloey turns stern and asks Thomas if he has told his friends about Luke. Thomas says that he has not told them and that he wants to help Luke and be his friend. Skarloey is satisfied and reverses down the line. He does not see Rocky lifting rocks across his track. Thomas shouts out a warning and Skarloey manages to stop just in time. Skarloey thanks Thomas who is pleased that Skarloey is able to trust him.
As Thomas works, Luke puffs out of hiding and pulls up alongside Thomas. Luke apologises for hiding and tells him that he was scared. Luke then asks Thomas if they can be friends. Thomas is very pleased and the two engines work together contently. Suddenly, the sound of a horn echoes around the quarry. This startles Luke who quickly goes into hiding. Winston whizzes around the bend carrying both the Fat Controller and Mr. Percival and pulls up beside Thomas. The two controllers thank Thomas for his hard work and tell him that Paxton is now fixed and will be resuming his usual duties at the quarry. With that, Winston rattles away. Thomas rolls over to Luke's tunnel and says goodbye. Thomas asks Luke about what he did to fear being sent away from Sodor. The little engine promises to tell Thomas if he tells no one else. Thomas agrees to keep the secret and Luke tells Thomas that it all happened when he first arrived on Sodor. On the boat he arrived on, there was yellow engine who spoke a different language that Luke could not understand. When they arrived at the docks, the men wanted to lift the yellow engine off first, but an excited Luke asks to be lifted off first. The dockers agreed. Luke pauses ominously. Thomas asks Luke to continue. Luke then tells Thomas that he knocked the yellow engine into the sea. Luke then recalls having to go to the Steamworks, but all he could think about was the yellow engine. The yellow engine was left in the sea for a long time and when he was finally lifted out, he was rusty and ruined. The yellow engine was never seen again and Luke assumes he must have been sent to the Smelter's Yard as he was not fit to work. Suddenly, Thomas hears Skarloey shouting at Paxton who bolts out from behind some trucks. Thomas questions what Paxton is doing and the Diesel stutters that he has come to take over from Thomas and Paxton speeds away. Thomas looks back towards Luke, but the little engine has vanished. Thomas calls a final goodbye into the tunnel and leaves.
The next morning, Thomas asks Toby to work on his branch line while he sets out to find the yellow engine. At the Sodor Dieselworks, Thomas spots loads of engine parts, but none of them yellow. As Thomas rolls out onto the forecourt, he hears something that makes his boiler run cold. Paxton is telling Diesel all about Luke and what he had done all those years ago. Diesel is adamant that he does not want an engine that is capable of knocking another engine into the sea on his island. He tells Paxton that they will tell the Fat Controller who will tell the Thin Controller and together they will send Luke away forever. Thomas does not want to hear another word and steams away as fast as he can. Diesel sees Thomas and tells Paxton that they must find out what tricky Thomas is doing.
As Thomas races down the line, he remembers that Luke had said the yellow engine was rusty after the incident. He concludes that a rusty engine would have been taken to the Sodor Steamworks. When Thomas puffs in, he asks Victor if he can recall fixing a yellow engine that had fallen into the sea and spoke a different language. Victor stops dead in his tracks and makes an exclamation in Spanish. Thomas realises that Victor was the yellow engine that had fallen into the sea. Thomas insists that Victor tell him what really happened. So Victor takes a deep breath and tells Thomas the story. It is the same story up until the end. Victor tells Thomas that a big wave broke the weak chains holding him to the ship's deck. Victor remembers calling to the dock workers, but they could not understand his language. As Luke was being lifted, he swayed on the end of the hook and knocked into Victor who could do nothing to prevent himself from slipping into the sea. Because of the bad weather, Victor was left underwater for a long time and when he was taken out, he was in a terrible state. As no one could understand him, Victor decided to learn English and, since he was in need of a repaint, his first word was "red" as that was the colour he wanted to be.
Thomas races away from the Steamworks, determined to reach the Blue Mountain Quarry before Paxton and Diesel. As he arrives, Luke puffs out from the quarry hills to greet Thomas who calls out that he has spoken to Victor about the incident, but he is unable to say any more. Skarloey interrupts him and tells Thomas that he had made a promise not to mention Luke to the other engines. All the engines are cross, including Luke. They all tell Thomas that he is not their friend any more. Then Diesel's horn echoes around the quarry and he pulls up behind Thomas with Paxton close behind. Diesel looks up and spies Luke at the top of a hill. Thomas tells the little engines not to listen to Diesel, but he knows the little engines will not let him explain his side of the story as they feel that Thomas has let them down.
Thomas puffs to the foot of the hill and begs Rocky to lift him onto Owen's platform so that he can reach Luke and explain to him. Owen starts to pull Thomas slowly up the hill. Diesel shouts up to Luke, telling him that Thomas cannot help him now and that he will have to leave the island. Luke believes Diesel and backs away as Thomas rises towards him. As Thomas reaches the top of the incline, he shoots off the platform to chase after Luke, but Thomas has forgotten that the lines in the hills are for narrow gauge wheels only. Thomas tries to back onto the platform, but his wheels cannot grip. Instead, Thomas rolls forwards and is soon hanging dangerously over the cliff's edge. Luke buffers up behind Thomas and declares that he must help his friend. Thomas laughs in relief, but he is not out of danger yet. As Thomas rolls onto Owen's platform again, Luke slips onto the platform too. The platform groans under the weight of two engines and gives way. The two engines hurtle towards the quarry floor at a tremendous rate. Owen tugs at the winch in order to slow down the platform. It finally bounces to a stop at a lower level of the quarry. All of the engines cheer and whistle; pleased that no one was hurt. However, none of the engines notice that Paxton has disappeared.
Suddenly, Winston arrives carrying the Fat Controller and the Thin Controller. The Fat Controller is furious to find Thomas causing confusion and delay at the quarry, instead of working his branch line. He orders Rocky to lift Thomas and Luke down. Diesel oils forwards to explain to the Fat Controller about Luke. Diesel tells the Fat Controller that Luke had pushed an engine into the sea. Thomas does not have time to reply before Paxton enters the quarry, pushing Victor on a flatbed. Victor has come to meet an engine he has not seen in a very long time. He tells Luke that he did not push him off the boat, he slipped off and it was an accident. Luke does not believe that Victor is the same engines as the one that plummeted into the sea until Victor speaks in his native language. Luke is happy for the first time in a long time and he tells the Fat Controller that Thomas is his hero and his friend.
A few days later, Thomas goes to the Steamworks. Luke is there with Victor who jokes that he has found a yellow engine. Rheneas then puffs out of the Steamworks smiling. He has been given a new coat of bright yellow paint. Thomas beams from buffer-to-buffer; a bright new colour really does mean a new life for his friends.