The episode begins with an old sage named Sodoramus arriving on Sodor via boat in 1545, 400 years before the beginning of the series. He foresees a series of horrific events that will occur on Sodor, with technology being the root cause. He concludes that the only way that man's misuse of technology can be prevented is if he sees himself in his technology. Sodoramus casts a curse on the island wherein all vehicles will become sentient as soon as they touch Sodor's soil. The rowboat he arrived on becomes sentient seconds after.
Part 1: The Piper Edit
Following the events of the previous episode, Phil and Robert are being held hostage in Phil's security bunker by Mason. Mr. Hugh lies dead in the center of the room with a knife in his back. In the corner, they see Stephen Hatt, wearing his real father Simon Johnson's clothes, holding Stanley Aardman hostage. Stephen has been planning his revenge against Phil since being released from prison and explains that he read up on Simon in jail. He decides that his destiny is not to run the Island of Sodor, but rather to destroy it as his father tried to.
Up at the quarry, Ryan is sitting quietly when Diesel 10, mistaking him for Thomas, comes up behind him and tries to push him over the edge. Ryan tries to explain that he is not Thomas, but Diesel 10 does not believe him. He is about to push Ryan over the edge when the real Thomas, having been repaired after his previous accident at the quarry, comes up behind Diesel 10 as Ryan is thrown off the tracks by Diesel 10's claw. Thomas tries to push Diesel 10 over the edge while Diesel 10 resists.
Meanwhile, back at the bunker, Stephen declares that it is not enough to just kill Phil; he must also kill his son to prevent him from taking over. Robert threatens to have his soldiers come and storm the bunker. It is then that Stephen reveals that the military base was entirely his doing: he hired two actors to convince Robert to build the base. He also reveals that he hired a man to get Bear and Diesel 10 from Lewis Packard. When Lewis wouldn't budge, Stephen orchestrated Ferdinand's boiler explosion that killed Lewis. Jenny was more agreeable and Stephen was able to buy the diesels. Stephen then reveals he installed a bomb into Bear after purchasing him, which is why his engine makes growling sounds. As Bear enters the military base, Stephen detonates the bomb, which starts a fire. Belle and Flynn are both killed by identical bombs as they hurry to the base, leaving nobody to put out the fire. The military base burns to the ground, killing nearly a hundred people.
Stephen turns his attention to Stanley and pulls out a gun. Phil begs him to not to do it, but Stephen murders Stanley. This causes Robert to snap. He breaks free and starts brutally beating Stephen. Phil warns him that Mason is coming behind him with a gun, but Robert is too late to notice this and is killed by Mason.
Thomas is still struggling against Diesel 10, saying that he does not have to win as long as Diesel 10 loses. He declares that he is avenging Lady, Edward, and Gordon. Ryan is horrified as Thomas tells Ryan to take on the mantle of #1. Thomas finally manages to push Diesel 10 over the edge of the cliff, but as he is coupled up to him, Thomas is willingly pulled to his death too.
Stephen orders Mason to complete his task. Mason grabs a machine gun and then leaves. Stephen grabs a knife and prepares to kill Phil. He impales Phil through the heart, but this does not quite kill him. However, he is unable to move as Stephen mockingly unties him and tells him he can leave. He pushes Phil over and begins stabbing him repeatedly with the knife, then tells him that he is going to kill Michelle and Anne after Phil is dead.
Michelle and Anne are looking for Stanley, unaware that he is dead. Meanwhile, Mason enters Maron Park and recalls the last time he committed an act of terror there. This time, he decides that his efforts will not be so futile. He pulls out the gun and opens fire, killing everyone in the park. He also shoots the policeman who tries to stop him. As he tries to leave, he is shot in the back of the head by another policeman.
In the bunker, Stephen is still stabbing Phil, who is barely alive. Stephen says that Phil's death will bring about a new era on Sodor. Michelle and Anne realize they have not checked the bunker, and as they enter, they scream in horror when they see Robert, Stanley, and Mr. Hugh lying dead on the floor. When Stephen sees them, he turns his attention to Michelle and charges at her with the knife. Phil is able to reach his arm out slightly and trip Stephen, who falls onto the knife, which impales him through the chest. Phil sees Michelle, who finds that he is unresponsive. He then succumbs to his injuries and dies.
Alan is made the new controller. A new addition is made to Maron Park next to the statue of Diesel: a memorial for Phil, Robert, Stanley, and the soldiers who died in the destruction of the base. Likewise, a memorial statue of Thomas is placed outside of Knapford Station. Ryan has decided to have himself repainted back to his purple livery, believing it would be wrong for him to wear the #1. All he wanted back when he arrived on Sodor was to replace Thomas, but thinks it feels wrong now that he actually can replace him.
The security cameras are taken down, the unsafe buffers at the quarry are blocked off, and after Alan retires and Anne is old enough, she becomes the new controller. To prove herself, she decides to relieve the railway of its shortage of engines. Her first act is to purchase a new one, which she names Stanley in honor of her brother.
Part 2: The Prophesy Edit
Circa 2020, the US is about to enter another war. An FBI agent named Craig Rogers questions an email he received from his superior about an island with talking trains. His superior asks him if he is familiar with Michelle Aardman, a British TV producer, who created a children's TV show known as Thomas the Tank Engine & Friends but has been dead for 4 years. When the director shows Craig a VHS tape, Craig recalls having owned the tape as a kid, to which the director responds that the show is not entirely fictitious. The director asks Craig to seek out Michelle's daughter Anne, who is now an older woman and still runs the island, to convince her to help with a project.
When Craig arrives on Sodor, he is surprised to see that the rumors of talking trains are real. He makes an appointment to speak with Anne and then leaves to look around the island. When Craig finally meets with Anne, he explains that he would like bring a few US military planes to the island so that they may become sentient. He says that by doing so, they will be able to operate more effectively than if they were normal planes operated by humans. Anne agrees.
The US military then begins constructing a hangar on the former site of the Stewart Barracks Army Depot. Some time later, the enemy finds where the Air Force has been hiding. Anne orders everyone to take shelter in Phil's long-abandoned security bunker underground. After multiple bombs are dropped, everyone is panicking, so one of the citizens pulls out her cell phone to play music to calm everyone down.
The series ends with a flashback montage of the engines working as the song "Que Sera, Sera" plays, leaving the fate of Sodor, its railways, and its people unknown.
- Thomas (death)
- Diesel 10 (death)
- Phil Aardman (death)
- Michelle Aardman (death)
- Robert Stewart (death)
- Anne Adina Aardman
- Mason (death)
- Stephen Hatt (death)
- Sodoramus (death)
- Craig Rogers
- Stanley Aardman (does not speak, death)
- Alan (does not speak)
- Belle (does not speak, death)
- Flynn (does not speak, death)
- Bear (does not speak, death)
- Stanley (does not speak)
- Lady (mentioned)
- Edward (mentioned)
- Gordon (mentioned)
- Turtles has said that the fate of Sodor at the end of the episode is open to interpretation. It is left ambiguous whether the island’s people and engines are killed in the air raid.
- Michelle Aardman takes the place of Britt Allcroft, the real life creator of Thomas the Tank Engine and Friends.
- When Craig is talking to Anne, he looks over to a poster of Oliver. This is likely a reference to his voice actor DaWillstinator (formerly known as missoliverandblossom).