One day, our heroes decide to take a vacation with Pooh Bear, Jimmy Neutron, Hiatt Grey's engines, Roary, Theodore Tugboat, and their friends. But Nyx finds an Alspark shard and gets info absorbed into her brain. Now the Deceptitrains are after our heroes, and a ressurected Megatrain kills Thomas. But if that wasn't bad enough, a reproggramed T-1000 is sent to kill Nyx by Princess Chaos 28 years into the future. But a reproggramed T-800 Terminator is sent back to protect Nyx. And more help is on the way from a dinosaur Trainbot. Now our heroes must find the "Crystal of Train-Primes" to bring back Thomas and stop Ultratron, aswell as the T-1000. But also keep a lookout for the "Cloggersaurus."
Beginning/The Story of Ultratron
The film begins with Optimus narrating about how Thomas become a Prime. And then later defeated many of the villains, and even how he helped him defeat Unicron. He also shares about 2 Terminators that were sent back to kill part of his family; The first was sent to kill Twilight Sparkle, his marefriend. But, it failed. The second was sent back to strike at Nyx, [who was recently adopted by them] But their future selves were able to send a protector for Nyx.
Then we see the Ice Age, and a robotic-like Carnotaurus scares off a herd of Mammoth and a Neanderthal hunting party [who was haunting the herd].
The T-800 and T-1000's arrival
Soon, near a bar outside Equinelantis, a reproggramed T-800 Terminator arrives. After entering a bar, it encountered a group of bikers, stealing one's clothing, M1911 pistol, and motorcycle and the bar owner's sunglasses and shotgun: A sawn-off Winchester M1887 lever-action. He then drives away. Meanwhile, somewhere else, a police officer responds to strange electrical disturbence but then is killed by a man who then takes over his idenity and patrol car.
Preparing for vacation
In Equinelantis, our heroes are preparing to go on a holiday with Pooh Bear, Jimmy Neutron, Roary, Theodore Tugboat, and their friends. As Nyx is packing, she finds an Alspark shard, then symbols are absorbed in her head. Then she drops it, which creates several tiny robots, but then they are destroyed by James. Nyx then hides the shard in a little container and hands it to Morley, before joining the rest of the group. But as they leave, a tiny Deceptitrain spy watches, and then gives chase. At the same time, the Terminator sees them and follows behind. Then the odd man from before comes up to the castle and asks 2 of the guards if they've seen Nyx, but they tell him that she went with her family on vacation. He then ubtangs a photo of her and then goes to find them.
Then the Constructitrains head for the sea floor and find Megatrain's courpse at the bottom, they then use one of a stolen alspark shard to bring him back to life. He then flies out of the sea, to who knows where.
At the vacation home
Meanwhile, our heroes reach the vacation condo. And there they meet Mike and Sulley. Later that night, they were having a blast in the disco room, but Nyx began seeing Deceptitrain symbols all around. But they had to call it short, because Bumblebee shows up, and snaps her out. Then Optimus arrives and tells them that another Alspark shard was stolen. Meanwhile back at the condo, Morley, Blitzer, and Rusty corner the Deceptitrain spy trying to get the shard Nyx found, but they lock him up in a boxcar.
After that, Megatrain manages to fly all the way back to the Deceptitrain ship, the Enimore. There, he reunites with his sidekick: Track Arachnis and The Ultratron. Ultratron then shares of his duty to rule once again. Then he shares of how Nyx had info from the alspark aborbed into her brain. Then He also shares that some beings back on earth have made contact with them and plan to help them out. The Deceptitrain leader then opens up a veiw screen and on the screen is Discord, Queen Chrysalis, their children, Dread-Steam, The Dazzlings, and Evil Jimmy Neutron and he talks to them.
Encounter with the Terminator/Canal chase
Back on Earth, the foals are heading to an arcade nearby. But as they head there, the Terminator spots them and follows close behind. As the mysterious man is asking citizens if they've seen Nyx, and then he is lead to the arcade. As the foals play many of the games the Terminator and the man are searching for them inside, [the Terminator has his shotgun inside a pizza box]. Then the man runs into Yuna, in which she warns Nyx and tells her to run. The man then follows close behind and he catches up to the filly at exactly the same moment as the T-800. Before it can shoot Nyx, the T-800 blasts him with his powerful shotgun, distracting him for a moment, allowing the other machine to shield her. The T-1000 retaliates by unloading his entire magazine into the T-800's back. While in the process of reloading, the T-800 blasts the T-1000 repeatedly, knocking him out and to the floor. It takes a moment to recover whilst the T-800 reloads and then springs to its feet and grabs the T-800's shotgun. They struggle for a moment before the T-800 grabs hold of the T-1000 and slams him into a brick wall. The T-1000 responds in kind, throwing the T-800 through another plaster wall and then hurling him through a window, much to the surprise of the nearby gamers.
The T-1000s pursuit of Nyx continues. Nyx speeds away on her scooter with the T-1000 in hot pursuit, running 5 times faster than any athletic human possibly could. Nyx escaped onto the main road and managed to put some distance between him and the T-1000, however, prompting the Terminator to steal a truck after throwing out the driver who was driving without a seatbelt. He then drove after Nyx, who once again escaped, fleeing down a levee.
The T-1000 was not to be deterred, however, and drove his truck off a bridge and into the embankment, once again initiating a chase, severely damaging the truck in the process. Nyx managed to keep ahead and the T-800 was not far behind on a bike of his own. The T-1000 almost lost his head whilst driving under a low bridge, but afterward he managed to close the gap between them and started to ram the back of Nyx's scooter. By this time, however, the T-800 had caught up and was attempting to overtake the T-1000's truck.
He tried to dissuade the T-800 but it managed to slip through regardless and rescued Nyx from her underpowered scooter, which got thrown to the side by the truck. The T-800 then shot out the truck's front-left tire, compromising the T-1000's ability to steer effectively, resulting in it crashing into a low bridge. The 100 gallon fuel tank ruptured and a loose cable spark triggered the vehicle's explosion, distracting the T-1000 long enough to allow for Nyx's escape. It emerges from the wreckage and stole another police car.
Somewhere in the city, the Terminator tells Nyx that he is a Cyberdyne Systems Model 101, reprogrammed by her future brother, 28 years from the future, to protect her. On their way back to the vacation condo, the Termator then shares with Nyx that the other guy is a T-1000 reproggramed by Queen Chrysalis' daugther, Princess Chaos. He also shares about the T-1000's advantages, such as him being made of liquid metal and having the ability to imitate anything it samples by physical contact.
Afraid that the T-1000 might go to kill her family, she orders the Terminator to help her evacuate her family. On the way, she makes him swear not to kill innoccent lives and only kill those who he is ordered to kill.
Changlings!/Escaping the T-1000
Back at the condo, the others were at the beach. But then the T-1000 takes the form of one of the guards outside, intending to get Nyx when she returns. She gets the symbols in her head again, and then as the others go back to their room, they run into Captain Thorn and some of the Changlings! But then as they went for the elevator the Terminator emerged from it. Most of the team was frightened to see him and they ran back. But then Nyx raced out trying to stop them. Then the Changlings jumped onto them and began binding them. Nyx then ordered the Terminator to help them. He then came up and then killed the other Changlings while Captain Throne was left stunned. Some more came in but Hiatt Grey's engines and Rattlesnake Jake jumped in and saved them.
But then the T-1000 came in. The team was shocked to see him and they ran as the Terminator provided cover fire. gave chase as they fled into an elevator, receiving a shotgun blast in the face at close range. It quickly recovered, pried open the empty elevator doors leading to the shaft and jumped onto the elevator roof, morphing his arms into swords to try and stab the group from above, one stab catching Anna on the shoulder. They lasted long enough to reach the underground parking lot and escaped the elevator. The group then jumped into a bus. The T-1000 formed a large blob and "poured" itself into the lift's interior, reforming into a humanoid form and giving chase once again, but was held at bay by constant gunfire by the group It managed to grab hold of the back, however, and smashed the rear window with its sword hook to get at Nyx, but the T-800 and Mighty Joe blasted it off the vehicle with their shotgun and Vulcan Gatling gun.
The Deceptitrains capture our heroes/Field battle
After that, a Chinook helicopter flew in and picked them up, Nyx is dangling dangerously. But is caught by Brian. The helicopter then carries them to an old ship yard and lowers them into the building. There Evil Jimmy walks up, and cuts the bus in half with the laser in his watch. Then Megatrain appears, then he throws Nyx onto a table, and pins her down. And Evil Goddard starts examining Nyx, and then sends a little drone into her ear and it scans her, and projects the symbols through her horn. Then Princess Chaos states that they need her brain, and she pulls out her knife and about to to start the operation when Thomas, the other engines, and the Autobots burst in. And Thomas battles Megatrain in a field, while trying to protect Nyx and most of the team. But then Megatrain kills Thomas!
Deceptitrains' Wrath/The King sends for help
After Thomas' death, Megatrain decides it's time for the Deceptitrains to show their existence and force the world to find Nyx for them, then the Ultratron arrives to earth and tells earth to find Nyx or else. Meanwhile, back at Equinelantis, Thomas' body is brought to the city and many of the Autobots are there too, then the marines arrive and surround them, they state that the Autobots should leave, as well as the Trainbots. King Solar Flare is devastated about the ordeal, and since the Marines won't copperate, he decides to call in the Wonderbolts.
After the chaos, Nyx grieves with Twilight hugging her, as she is weeping herself. While the Terminator stitches the slash on Anna's shoulder. Then as Mucker removes bullet slugs from the Terminator, the others explain about their encounter with Terminators and the T-1000. They then later decide to reset the Terminator's chip so he can learn to be more human, but when they remove the chip, Twilight attempts to destroy it but Nyx stops her. After they place the chip back, the Terminator explains about the future and what lead to the T-1000 being lead back to kill Nyx. Then Nyx decids to turn herself in. But the Terminator declines and sates that it's better to try and stop the Deceptitrains on their own. Twilight agrees, but then she turns to Railan and Trax and asks them if they can read the symbols but they can't, they even ask the Terminator but he can't ethier. But then Jimmy then reveals that he might have some copies of the symbols in his lab.
Getting answers/The Train Musesum
The next day, they head to Jimmy's lab. And Jimmy shows them some Deceptitrain symbols he's collected, and they are equal to the ones in Nyx's head. However, none of the Trainbots know what they mean. Blitzer doesn't even know them because he's been stuck in a spaceship for most of his life. At this point, reveal Morley, Blitzer, and Rusty reveal their captured Deceptitrain. Who's name is "Tronie." And he explains that the symbols are the languge of the Train-Primes, and he then shows on a map where they can find one guy who can desipher them.
So they all head to a train musesum, and Tronie leads them to a really old steam locomotive. Nyx then uses the Alspark shard and awakens the really old Deceptitrain. He then starts walking outside searching for something, but the group stops him.
Steamfire's story of The Ultratron
At the mountains of Equestria, our heroes come out. Then Steamfire shares about The Ultratron, and tells them that only a Train-Prime can defeat him. He then gives Nyx a clue about the symbols that could lead them to the Crystal of the Train-Primes, "When dawn a lights the dagger's tip, the archer will reveal the way." and warns her about a Trainbot that guards the tomb, and then he tells her to run, before Megatrain finds her.
Morley's story of the Cloggersaurus
On the way, Morley then states that they should watch out for the Cloggersaurus. He explains that it is a huge hybrid dinosuar that resides in the mountains and guards the outside of the caves that lead to the Tomb of the Train-Primes. He explains that it has the body of a T-Rex, the spikes of a stegasuarus, and huge arms. And that he is often heard growling.
That Night/The 3 valleys
That night, a mist rolls in. And our heroes have to slow at an amber signal, and they see a sign saying: "Keep out! Turn back, go to jail, or worst rest in peace". And they saw a fog mens coat! Realizing there getting close, so our heross decied to make camp, then the Terminator shares with Nyx more detail about Princess Chaos' motovation to send the T-1000 back to kill her. Then when dawn hits, Nyx saw a coranation of starts that looked like an archer, and wakes up everyone and tells them they found the way. The next morning the team are now outside three valleys. In which they all lead to the caves. However the team have troubles choosing which one to go down. Nyx is is thinking about the reasons of which would work, but then Cindy yells, "CHOOSE ALREADY, NYX!!!" But Cindy's outburst then starts a landslide, in which the whole reach into each valley as the landslide blocks the way. Now the whole team is split into 3 groups. Inside the first, Nyx finds that they've al seperated, so they decide to continue on and reunite in the caves. They also find that Stephen's lost his funnel.
Journey through the valleys
Morley then starts to regret talking about the cloggersaurus, and then they hear a growling sound. Then run off in fear! But then Mighty Joe manages to calm them down and remind them that the world and solar system are at stake. Soon enough, the group soon enter the caves. Then they hear the growl again, in which they jump in fear. But they continue on. Then they spotted an old pipe lying aside the track, and they use it for Stephen's funnel.
In the caves/some split up
As they continue, they soon reach the caves. Inside some members of the groups split up. Then when they hear a str ange whistle. Then with one fo the groups the engines hit some overgrown roots, and one that looks like a Tricerotops' head falls and lands on T.C.'s face. At first the other are scared but then they have some fun. Then they hear the growl again, in which Hugs backs up into some old trucks which couple themselves on. [But Hugs doesn't notice] Then Rabbit meets up with Felix, Spongebob, Brian, Twilight, Cadance, Mike, & Hiatt Grey, but then they fall down a hole in the ground and tumble head over heels down tunnel. The Tigger reunites with Vanellope, Ralph, Sagwa, Sheegwa, Inuyasha, Vinnie, and Rarity. Then as they continue, a bunch of bats spook them and they run down the tunnel. Meanwhile, Piglet, Fluttershy, C-3PO, R2, and Sunil [who are running after hearing the whistle] start splipping on pebbles and then fall over a cliff side and land on Hugs' cab roof, spooking the tramway diesel. Then that group take off at full speed [and they hear the trucks following but think it's the Cloggersaurus.] The others are going through their tunnel, they soon hit a downhill and are going at fast pace.
Meanwhile, Brian, Vinny, the human mane 5, the Terminator, and the foals [whom Skyla is still scared about the Cloggersaurus] stumble to a boneyard in one of the caves. Completly paranoid of every sound Skyla hears is properly the hybrid creature, but soon she sits on a rock then notices some oil. She then looks up and there were rows of teeth! And yells: "THE CLOGGERSAURUS!!!!". Then out came a robot Carnotaurus that breaths fire! Brian, Vinny, and human Rainbow Dash manages to distract it with their hand guns. But the beast hits her with his tail, and pursues the foal. Then the robot beast hears Sunil screaming and follows it.
While in a big room, Pooh starts walking behind some crystals, as then Felix, Spongebob, Twilight, Cadance, Mike, & Hiatt Grey fly out the end of the tunnel and hit the ground. Then with the fleeing group they see their heading for a tunnel entrance and they brake hard but slide on the slick rails, [T.C. then loses his mask while they fly through the entrance]. Back in the main room Felix, Spongebob, Twilight, Cadance Mike, & Hiatt Grey look up and see the other groups racing in from each of the different tunnels in which they all crash into each other. They soon untangle themselves and find the trucks Hugs was pulling and the timid beings are still on her roof. Thrn the human mane 5 run up, and explained they saw the Cloggersaurus. Then they hear the growl again and there, they see the Cloggersaurus [which is actually a distorted Pooh through crystals]. So they run down another tunnel, as Pooh slides down a slide. As they continue to run, they then end up at dead end cliff edge. As Pooh gets stuck in creveze. In whch they think the Cloggersaurus got him.
The Tomb of the Train-Primes
Then up above, they see the tomb of the Train-Primes! However, there is no way on their cliff to get up to the tomb. Rabbit then manages to think of a plan to get there, and he wants Tigger to bounce Piglet and Sunil up to the ledge and then they drop a vine hanging over the side. Tigger, Piglet, and Sunil at first doubt they can do be they give it go for Thomas.But when Pooh breaks free he slides down into a a giant cavern of diamond, and then he heard a strange roaring sound, and there, right in front of him was a giant Trainbot dinosaur! And then Pooh finds another tunnel and starts walking down it, but soon came to a dead end. But the Trainbot dinosaur transformed into a tank engine and starts banging on the rocky wall. Soon enough, everyone else makes it onto the ledge, and then a mysterious figure comes towards them. And it reveals to be Lady! She explains she has been following them to help them get Thomas back and stop Ultratron. Soon they find the Crystal of the Train-Primes, but once Nyx picked it up it disintegrates to dust. But the young filly refuses to give up and pours the dust into a small bag she uses for keeping coins. They soon find some old railway tracks in the tomb, so they ride them out.
Journey on the old rails/Train chase
After riding down windy rails and hills they reach the outside, but beneath them a driller train chases them. And in the cab is Evil Jimmy, along with some of the Changelings. The trains race across an old double decker bridge, however due to it being poorly built, the upper track with our heroes is collapsing because the driller train's width [which is on the lower track] is causing the support beams to pop loose as the track behind it collapes. But soon the 2 trains are side-by-side and Sheen accidently ejects Skyla who lands on the driller train. And gets dazed and she slips out where they're going to Evil Jimmy. But as our heroes go over the driller train, Pepper Clark grabs Skyla. As the trains continue speeding down the rails, the driller train then manages to get behind Percy and Evil Jimmy opens the regulator to full power, in which the drill starts grinding against the back of the brakevan. But then the pressure gauge hits the blue bit with the skull and crossbones, and the driller train explodes! But then our heroes find the track is ending straight at an uncompleted bridge, they drive through the warining sign and went flying! Then, they landed on the sand. Skyla then admits that she acidentally slipped out about the crystal to Evil Jimmy.
Race for Thomas/Decastator!
Then later an engine comes out of the cave, then Pooh hops out. The Engine then transforms into a Carnotaur. Percy insists his help, but first he refused to obey Percy, but after he defeats Crusher in single combat, he respected him and assists him to save Thomas in exchange for his freedom. Back down the line, Evil Jimmy and some of the Changlings who didn't die recover from the wreakage, and they go to tell the other villains about the Crystal. Back with our heroes, they continued on their way to Thomas, then they see helicopters and planes fly above. And it was NEST, the Wonderbolts, and the other Autobots and Trainbots. They were all at pillars then, Evil Jimmy (on his speeder bike) follows and then contacts Discord and Queen Chrysalis. Then he fires his lasers, leadind the group to hide. They then split up, but before they can set off a huge army of Changlings is just outside, but the Terminator uses a minigun to take down the whole army, and everyone sets off. The Terminator then grabs a SWAT van nearby and drives toward Thomas, and everyone else goes another way. Then the T-1000 sees them and takes a nearby chopper and chases them. Meanwhile the others then come upon a bunch of diesel engines and then the disesl combine into Decastator! First our heroes were confused, beacuse they killed him years ago. Decastator then reveals that many Deceptitrains and the Constructitrains find his parts and rebuilt him. And then he starts sucking everything then Sheen and Penny Ling starts getting sucked in, and they are sucked into his mouth. But Penny Ling busts them out.
Soon Cruncher battles Decastator, and he fires a huge fireball at him. But Decastator slams him to the ground. But Cruncher fires another fireball and flees.
The Helicopter and Tanker chase/Battle continues
As the SWAT van continues down the road they see the chopper not far behind. Twilight then takes one of the assualt rifles and starts shooting at the chopper as the T-1000 returns fire. After a few gunfires, Twilight is shot in the leg. The Terminator then slams the brakes on and the chopper rear ends the van and crashes, then the van hits a car causing it's left tire to blow and the van topples over. The T-1000 extricated himself from the wreckage and wasted little time stabbing a concerned truck driver in the chest and steals his vehicle, which was pulling a tanker of liquid nitrogen. The T-1000 chased the group, almost forcing them off the road several times, and inadvertently directing them towards a lava temple [like the one from the Jungle Book 2].
The T-800 climbed across the car and onto his truck, firing a rifle into his face and grabbing the wheel, causing the truck to topple on its side and the momentum carrying it into the temple where the tank cracked open, spilling its contents. The T-1000 staggered out of the truck, covered in liquid nitrogen, and ambled towards the group, its body rapidly freezing. The more it persisted, the worse off it became, as his legs cracked and fell apart and his right arm then broke off entirely.
He examined his arm in shock as it froze completely and ceased all movement. The T-800 then shot it, shattering his body into tiny mercury-like pieces that scattered across the floor. This might have been the end for the T-1000, were it not for an overflowing vat of lava, the heat of which restored the pieces to their liquid form. Each droplet started to merge with others, quickly forming a large puddle, imitating the appearance of the element Mercury, from which it started to solidify.
Once it was fully reformed, the T-1000 resumed his hunt for the group, but started to suffer glitches, a malfunction caused by the liquid nitrogen, resulting in its feet and hands taking the form of whatever they touched. It was hardly concerned, and quickly caught up with them, resulting in another direct confrontation with the T-800. It surprised the older model and displayed his superior adaptability in combat and trapped the T-800 in a huge rock pile, crushing its left arm. Meanwhile the Autobots and Trainbots continue to battle as well as the NEST and Wonderbolts.
Killing Decastator/Race to Thomas
Decastator then starts climbing up a pyramid top, but Brian grabs a radio and pursues him. Then orders to have the Navy use a railgun on Decastator, which they did so, which kills Decastator. Meanwhile, Nyx's group contines racing for Thomas but a Construcitrain stops them in their tracks. James then appears and battles it, and then kills it. Percy then arrives and drives them closer and closer to Thomas, Cruncher then starts killing some of the Constructitrains by using fireballs and ripping them apart. But then the Changling train appears. Cadance and Chrysalis then get into a sword duel as the trains continue on, Evil Jimmy appears and incapates Jimmy. Percy then manages to put some distance from the Changling train. Soon the other come up and they continue to Thomas, Jimmy gets back up then he kills his evil clone with his zap watch. Back at the battle, Nyx countinues to Thomas. But then air strike comes in, Megatrain appears and he shoots Nyx, as the others run up. Twilight grieves for the lost of her daughter.
Nyx brings back Thomas/Killing Ultratron/The T-1000's death
Then in another deminsion, the Train-Primes visit Nyx and they ressurect her. Once Nyx woke up, she embraces her mother. As the crystal restores, Nyx then takes it and places it in Thomas' chest and Thomas awakens! But then the Ultratron appears and takes the crystal. And heads towards to his machine, Steamfire tells Thomas to take his parts and then tears out his spark. Jolt activates Steamfire's parts to Thomas, and flies off. But as he goes, the T-1000 then sought out the group, a menacing ripple flashing across his body, and managed to corner Twilight alone, taking a shotgun blast straight through its right eye before impaling her on a finger sword. The T-1000 demanded she call out for Nyx, but Twilight refused and her torture was interrupted by the T-800, who drove a pipe through his body.
Frustrated and visibly annoyed by the T-800's constant interference, the T-1000 ruthlessly struck the machine repeatedly with the pipe and smashed its head several times with heavy machinery, including a massive ingot of steel hanging on an overhead crane. As the T-800 attempted to crawl towards its M-79, the T-1000 drove the pipe into its spine and twisted it around before driving it deeper, destroying the machine's main power core. It is obvious that the T-1000 is at least 5 times stronger than the T-800.
Thomas then battles the great Deceptitrain leader after destroying the machine, critically injuring Megatrain in the act, using his cylinders to send Megatrain flying through some ruins. During the battle, The Ultratron pulled off the left cyliander, using them to strike Thomas in the face, but Thomas ultimately triumphed and ripped out the Ultratron's spark core, killing the treacherous Train-Prime.
With the T-800 seemingly disabled, the T-1000 took the form of an injured Twilight and called Nyx, who responded to his cries. Before the T-1000 could stab his target, the real Twilight arrived and shot the fake with her shotgun. The T-1000 returned to its default cop form and faced off against Twilight, who blasted him to the edge of the ledge, almost knocking it into the river of lava below. Her shotgun ran out of shells before she could finish the job.
Before it could advance, the T-800 arrived, having used its heat sinks to power a second back-up power cell. It fired a grenade into the T-1000's chest, whose mouth opened wide in shock as the projectile exploded within it, severely contorting his form. Unable to recover in time, the T-1000 lost its balance and toppled into the lava. The extreme heat rapidly-decimated its molecular structure, and it changed from shape to form, trying desperately to adapt to the deadly 760°C environment.
It proved futile, as the steel corrupted its design and melted its body. It gave one last metallic scream of mindless terror as it literally turned itself inside out, vomiting forth its own face from within before dissolving into nothing, its mission a failure and its existence ended.
After that, Megatrain, Discord, Chrysalis, and their children then leave. As Thomas then dettaches Steamfire's parts. Mucker drops the CPU and the arm of the first Terminator [from Thomas' Adventures in Transformers Prime] into the hot liquid. Since the Terminator had a computer chip in it, it also planned to destroy itself to prevent its technology from being discovered by other villains to find and use for their armies. Nyx begged it not to be destroyed, but it had to fulfill its mission. Yuna also reminded her that they still had the other Terminator too. When Nyx cried, the Terminator understood why, but could not cry itself because it was a machine. It hugged Nyx for the first and very last time, and having finally earned the Sparkle's respect, shook their hooves offered to a brother warrior. The whole team sadly watched as it is lowered into the lava below, the Warrior of Steel-in-Flesh gave Nyx an encouraging thumbs up before sacrificing its life for Equestria's future. Then, Bill and Ben were in relief that they didn't ran into the Cloggersaurus, at this point Morley confesses he made the whole thing up and they is no Cloggersaurus, at this point Cadance, Shinning Armor and some of the engines beat him up. Then Percy sets Cruncher free and he flees to an unknown location. They head their way home, While Optimus sends out a message.
- This film is based off the movie, "Transformers: Revenge of the Fallen" with a mix with "Terminator 2: Judgement Day" and "Pooh's Grand Adventure".
- This marks the first appearance Track Arachnis, The Ultratron, Constructitrains, Smoke and Sparks, and 2 good Deceptitrains; Steamfire and Tronie. And the Dinotrain: Cruncher.
- Mike Wazowski, James P. Sullivan, Pooh and his friends, Jimmy Neutron and his friends, The T-1000, The Human Mane 5, Megatrain, Decastator, Discord, Queen Chrysalis, Princess Chaos, Discsalis and Evil Jimmy guest star in this film.
- Starsmoke is mentioned in this film.
- Lady makes a special apperence in this movie
- At one point of the film, Stephen loses his funnel and goes funneless until the end of the film.
- Begining/The story of Ultratron
- The T-800 and T-1000's arrival
- Preparing for vaction
- Megatrain's resurrection
- At the vaction home
- Megatrain's return
- Encounter with the Terminator/Canal chase
- Changlings!/Escaping the T-1000
- The Deceptitrains capture our heroes/Feild battle
- Deceptitrains' Wrath/The King sends for help
- Taking shelter/Explanations
- Getting answers/The Train Musesum
- Steamfire's story of The Ultratron
- Morley's story of the Cloggersaurus
- That Night/The 3 valleys
- Journey through the valleys
- In the caves/some split up
- The Tomb of the Train-Primes
- Journey on the old rails/Train chase
- Race for Thomas/Decastator!
- The Helicopter and Tanker chase/Battle continues
- Killing Decastator/Race to Thomas
- Nyx brings back Thomas/Killing Ultratron/The T-1000's death
Songs and Soundtrack
- Music Score: The Terminator 2: Main Title
- Music Score: Transformers: Revenge of the Fallen: Main opening
- Bad to the bone [when the Terminator gets his clothes, his weapons and his motorcycle]
- Stadium Rave A [Spongebob Jellyfish Jam] - the music playing in the disco room
- Music Score: The Terminator 2: Escape the T-1000
- Music Score: The Terminator 2: Sarah on the Run
- Music Score: The Terminator 2: Escape from the hospital
- Music Score: Transformers: Revenge of the Fallen: Captured
- Music Score: Transformers: Revenge of the Fallen: Forest Battle
- Music Score: The Lord of The Rings: The Fellowship of the Ring - Gandalf Falls [when Thomas dies]
- The Headless Horseman Song (Cloggersaurus song) - Morley
- Soundtrack: Kevin MacLeod - Oppressive Gloom
- Wherever you are - Nyx
- Soundtrack: Thomas and Friends: Mail train theme [when our heroes are driving towards the direction]
- Sir Handel's song [from Special Funnel]
- Boo, Boo, Choo, Choo! - our heroes [while there in the cave]
- Soundtrack: Cruncher's theme
- Music Score: Shrek - The dragon [when Skyla first sees Cruncher]
- Music Score: Disney's Dinosaur - Breakout [When Cruncher and Pooh break out of the cave]
- Music Score: The Terminator 2: Judgement Day - "Trust me"
- Music Score: Thomas & Friends Misty Island Rescue - "The chase" [when Evil Jimmy and Dread steam are chasing our heroes]
- Music Score: The Terminator 2: Judgement Day - "Helicopter chase"
- Music Score: The Terminator 2: Judgement Day - "Truck chase"
- Indiana Jones theme [when James battles the Deceptitrain]
- Music Score: Transformers: Revenge of the Fallen - I claim your sun
- Music Score: Transformers: Revenge of the Fallen - I rise, you fall
- Music score: The Terminator 2: Judgement Day - "It's over, Goodbye"
- Music score: Disney's Dinosaur - Epilogue
- End song: Wherever You Are - Vonda Shepard & Barry Coffing