Thomas: Uh, that is to say we were seperated, and uh...
Trevor: Not daddy Globox?!
Peter Sam: We want our daddy! (the five children cry at Thomas sadly)
Thomas: (smiles, worried) Now, don't worry, kiddies. I'll bring your dad back. But first, I've got to find Emily. She loves to hang out around here. Have you seen her? (confused) What?
Percy, Skarloey, Rheneas, Trevor, and Peter Sam: (still crying) The mean old pirates took Emily over there!
Thomas: Hmmm... I've got to set her free! (runs away through a long tunnel) I can climb between these two walls when I go between and grab on. I'll repeat all the time until I have reached the very top. (speeds up the mountain, collects the fifth yellow lum, reaches the top with a purple lum behind him, which means he'll come back here later for a surprise. Thomas shoots a cage, which frees seven engines)
Donald: Splendid, Thomas! I'm king of the engines, I'll congratulate you for your bravery. (Douglas comes up to Donald and snatches the crown of his head) Hey!
Douglas: Don't listen to him! I'm the king of the engines!
Thomas: But... (Bill comes next to Douglas and snatches the crown)
Bill: No! I'm the real king!
Thomas: Come on, who's the king?
Bill: It's me! (Ben comes up next to Bill and snatches the crown until Bash, Dash, and Ferdinand begin with Donald, Douglas, Bill, and Ben over the crown)
Bash: Me, me!
Ben, Bill, Douglas, and Donald: No, me!
Thomas: Grrrr... STOP! I absolutely must see Emily. Do you know where she is? (The engines suddenly stop after getting frightened by Thomas, and at the end, Ferdinand is given the crown, and speaks quietly)
Ferdinand: Uh, that isn't easy to say, but I do have to tell you this. The pirates have taken Emily to the Princess Glade, and have locked in their one strongholds. To find her, you'll have to go through the Isle of Doors. The Isle is a magic place, which leads to many other worlds. Only the engines, that's us, know how to get there. The passage requires five lums, but I see that you have them. Prepare yourself for a great journey. (claps his hands as a silver lum appears on the ground and turns into a spiral door. Thomas gulps and backs away, scared. He runs forward and jumps in the portal and vanishes)
Emily: Thomas, you're our last hope. (Thomas arrives at the Isle of Doors and runs up from the First Clearing level to the second Princess Glade level. He dives into the sea and swims underwater)
Thomas: I can swim, using the depad control, dive, using the dive button, and resurface, pressing the a button. I must grab the blue lums, which are full of air as well. (Thomas swims into a cave to free a cage with five orange lums to pick up before he swims back out of the cave. He jumps up onto a mushroom, grabs onto a hanging wall to collect a yellow lum, climbs across, jumps off, and dries himself off. He races through a long tunnel over a river after getting a green lum as a checkpoint) Swimming is not advised. If I need some energy, I'll grab the red lums. (Thomas climbs up over the river and comes to a switch to activate it to open up a door, next to Thomas's three narrow gauge friends, who want their daddy back. He puffs across, collecting another yellow lum, until he climbs to bust a cage to free another yellow lum. He goes up past the engines, who are begging him to get their father back)
Skarloey: Hurry up, Thomas!
Rheneas: We want our daddy back!
Peter Sam: Don't be discouraged! You can do it!
Thomas: Okay, okay. If I take that green lum, when I die, I'll respawn back to where I was. (gets another green lum as a checkpoint and keeps on puffing down the line until he sees a drawbridge up ahead going up. He starts chuffing faster, jumps over the cliff, then hits a pirahna, and just makes it, but nearly loses his freight cars, which fortunately jump and make it too. Thomas flies over the hill, but flies down toward a platform, and safely jumps on a floating stone, which takes him around to get another yellow lum. He jumps back up, climbs up once again, and makes it into the next area. He arrives at the next area, but seems to find a black catterpilar coming toward him, and escapes him by climbing up. He slides down a slope, and comes to another area, which means that this level is where he has to come back later to get the last cage in the level. He climbs across the river, collecting another yellow lums, and lands in another area, which leads him to a strange prison ship. Thomas looks up and sees Den, who spies him, and jumps down to attack him. Thomas runs away through a cave, which leads him into a safe place. He climbs up, collecting two more yellow lums, five red lums, shoots a cage to get an orange lum, and collets another yellow lum) There! (jumps down and flies onto each lily pad to get two more yellow lums before he heads out of the cave and back to the prison ship where Den is waiting to kill Thomas by throwing fire barrels at him)
Den: STOP THERE, NOBLE TRAIN! (throws a barrel at Thomas, who ends up standing on the patch, and jumps out of the way, then jumps down a hole into the emptiness below to get a green lum) DON'T YOU KNOW THAT WE'RE THE CHAMPION PIRATES, WHO SELL FRIGHTENED ANIMALS TO THE SALT MINES AND THE CIRCUS?! WHERE DID HE GO?!?
Thomas: I must use my shadow and my helicopter. (jumps over the barrels, but activates his blue lightsaber, and swings at Dart, who gets his arm cut off, and pushed into the sea after Thomas defeats him) Look at this web. I can grab onto it. (Thomas carefully climbs up, dodging barrels, and jumps up safely without getting hurt. He shoots a patch on the door, which breaks down, before he walks inside. He now looks up at the switch, only to see Norman fast asleep. He sneaks quietly outside to meet up with Harold, who advises him to be careful)
Harold: Careful, there are lots of pirates in the area. There's a good chance you'll need to fight one! To move around during combat, keep the target button pressed down. This will allow you to keep your enemy targeted and make it easier to avoid his shots. (Thomas walks up to find Emily, but is stopped when Arry jumps out of nowhere and attacks him. With their two lightsabers lit, Thomas and Arry begin a furious battle, with the air humming and sparks fly as lightsabers swing and clash, until Thomas finally cuts Arry's hand off, knocking him out, cold. Thomas walks inside to find a powder keg he can use)
Thomas: I can use this powder keg by placing myself in front of it and release the analog button. Take this, Sidney! (throws the barrel at Sidney, who is surprised and whacked on the head, and knocked out, cold. Thomas takes the powder keg back to a patch on door and breaks it down, only to free an orange lum from another cage, and rushes back to the next part of the prison ship, climbs up a ladder and onto a net, jumps down, hops onto a trampoline to activate a switch to open the door, but gets nearly hurt by electric beams, and jumps up. He leaps across some alarm beams again, but manages to defeat Norman by taking out his pistol gun and shooting him on the belly, causing him to pull the switch for Thomas to jump, and walk through into the next area) Well, it's about time! (rushes through the area, jumping over two more electrical alarm beams, but accidentally falls down a hole, and walks alongside Emily trapped inside a stronghold)
Emily: Please, free me, Thomas! Encounter with that machine! And then, destroy it!
Thomas: No problem! (rushes through the cave and force chocks another robot pirate named Splatter, and throws the diesel against the wall, but throws him into the sea into a machinery room. He grabs a green lum at a checkpoint picks up a keg and takes to the patches on the machine to destroy it) Now this sounds like an easy rock puzzle to pull through. I can throw this in the air with the A button, and throw it in front of me with the B button. It's unsimple to take this keg and throw it at the patches, bombs appear and harass me if I attempt to move these kegs and take to the machine. My best suggestion is that I may want to throw it in the air while moving and shoots the flying bombs out of the way when I throw the kegs at the patches until the machine is destroyed, so I must repeat this, until the machine is destroyed. (picks up every keg, takes it to the machine, throws the kegs up, shoots the bombs, and throws the kegs at the patches until the machine is completely destroyed. The stronghold is down as Emily awakens and comes down in front of Thomas, worried, who stops in front of her) Emily, are you okay?
Emily: Oh, Thomas, at last! I was afraid Edward had failed.
Thomas: (depressed) He gave me the silver lum, but we got seperated. I need to find him and get rid of the pirates. But, to do that, I'll need all of my powers.
Emily: I am too weak to give you back all of your powers. They broke the promidal energy core into 1000 lums. And combining the energy has become very difficult. But, there may be another solution... Have you ever heard of James?
Thomas: (puzzled) Um... No?
Emily: He's the spirit of the world, and his powers are immense. He could help you defeat the pirates. Unfortunately, he has been sleeping for many years. But, there is a legend, which says, he could be awakened. If you reunite the four masks...
Thomas: (confused) The four masks?
Emily: These masks are magical and very powerful, and are hidden in secret and mysterious places. Now find them, Thomas, you're our only hope. I'll help you by giving you all the energy I've gathered. (laughs, creates a silver lum, which flies toward Thomas, and builds up in him, when he is surprised, and astounded)
Thomas: A silver lum? I'll have a new power? (laughs when the energy builds up in him) Yahoooo! Ha!
Emily: Good luck, Thomas. Bye! (vanishes in a silver lum and fades away as a purple lum appears above Thomas) Now you may grab onto the purple lums.
Thomas: Impressive. Goodbye, my lady. Let's get going. I can shoot the purple lums to grab and jump off to let go. (climbs up a net to collect two more lums before he shoots the purple lum to swing across. He jumps over a laser beam, which nearly zaps him, jumps between two walls to collect two more yellow lums, races underneath the laser beam, jumps down a hole, lands a pipe, and runs into the next area)