- Pages 3-5: Movie starts off on July 20th, 1969 with the moon landing. They then cut off the signal; this is the scene from the announcement trailer. We see a close-up of Sentinel Prime's face.
- Page 6: We then cut to a suspected rogue state nuclear facility in the middle east in present day. We have the usual Optimus Prime voice-over: "We are not alone. And that has not been easy to get used to. For too long, we Autobots held the evil Decepticons at bay, ourselves. But as war spread from the dying planet Cybertron to our new home on Earth, we found something unexpected: Allies." There's a shot of the Defense Minister's car, followed by Bumblebee, Sideswipe, and Mirage all in vehicle mode. The guards let them in but are confused by the entourage of the Autobot cars. We see Mirage transform and the others in the background transform, and Mirage says, "Don't move and you don't have to die today."
- Page 7 is missing.
- Page 8: There's an explosion and the four Autobots are seen walking away from it. They are Mirage, Bumblebee, Wheeljack, and Sideswipe. Wheeljack calls to base, and says the mission is accomplished. We then see the decommissioned N.E.S.T. HQ in Diego Garcia. Optimus Prime at base tells Wheeljack to head back to Washington and that Optimus and Ratchet will be along when they finish closing down the old base. Optimus' voice-over continues: "While we track down stolen weaponry, Colonel Lennox believes he has a lead on the location of a recently surfaced foe. A foe whose crimes I vow shall not go unpunished. My fallen friends won't pass to the next life alone." Optimus Prime looks over at some crates labeled with the names of dead Autobots: "Knockout, Elita-one, Dune Runner, Blazemaster, Armorhide, and Jolt". He specifically looks at the picture of Elita-one. Colonel Lennox asks Optimus Prime if he's ready. He says Ratchet is onboard the C-17 and they're ready to head to Ukraine. Optimus Prime says he's ready and also hopes his contact is correct. Lennox says it's time to play hero again.
- Page 9: In Washington D.C., we see Carly wake Sam up and give him a stuffed animal bunny as a good luck charm and says he's getting a job today. Sam jokes and says she should just give him the rabbit's foot, and Carly says that's just mean to take a foot off of a rabbit. Sam talks about how demoralizing it is to have saved the world twice and is now groveling for a job. Then the small robot named Brains (from the prequel comics) jumps out from behind the bed and says, "Yea-- I guess we know who wears da pants in dis family!" Sam pushes him away and Carly leaves the room saying, "You're not normal, Sam" and Sam replies with, "That's why you love me." Carly leaves by saying, "Not love, yet. We'll be closer when you can cover your half of the rent. Now-- go get a job!"
- Page 10: Sam escorts Brains back to the doghouses (for Frankie and Mojo). Brains tells Sam that Carly has to learn to live with them (referring to himself and Wheelie), so he has to pick. Sam picks Carly. Wheelie complains and says that he was there for Sam when Mikaela dumped him. Sam asks them if they ever wondered by the other Autobots don't want the two of them around. Wheelie says they're wasting their talent, and Sam replies with, "yours and mine both."
- Page 11: We then go to Prypiat, Ukraine. Ratchet and Optimus Prime are in vehicle mode. Ratchet jokes to Optimus saying that they've been to some beautiful places on Cybertron, but the wasteland here takes the prize. Optimus Prime asks if Cybertron was any better when they were done with it. We see Colonel Lennox ask if they enjoyed the tour. He says the city has been uninhabited since 1986, and the only way for humans to survive the radiation is with the suits they're wearing. A guy named Voskhod isn't wearing a suit and says it's only a matter of time for him anyways. Voskhod says that every year they dig deeper, but this year they found it (we don't know what "it" is yet). He says to follow him, but first he says he must tell Colonel Lennox something. Something flies overhead and Voskhod says that perhaps that can wait. Lennox tells Voskhod to keep no secrets. Voskhod says that Lennox doesn't understand this part of the world, and that if they're found, his country will deny he ever existed, just as they do the aliens at the heart of Chernobyl (we know Shockwave is kept there, so that may be who he is referring to).
- Page 12: They come upon something and Lennox says the object looks extraterrestrial and that it's in some kind of harness. He wonders why it has Soviet Space Program markings. Optimus Prime says that that is not the question they should be asking. The ground starts to shake and Voskhod says, "No, no-- not now..." The tentacle creature appears from the ground and starts attacking, and it kills some humans.
- Page 13: Everyone runs out and Ratchet tries to stay with Optimus Prime, but Optimus tells him to leave and that this one is his. As they leave, Lennox asks Ratchet if that's what he thinks it is. Ratchet says that it's a Driller, "the most feared and terrible beast on all of Cybertron, and worse..."
- Pages 14-27 are missing.
- Page 28: Laserbeak is chasing Sam through a building firing away. Sam has an axe. He's angry at always being attacked and not being able to understand Laserbeak's language. He gets on a table and slams the axe into Laserbeak. Sam's boss walks in, Sam says he doesn't think he'll have those files ready by three -- and can he take the rest of the day off? Laserbeak reports to Soundwave.
- Page 29: We're now at N.E.S.T. operations in Washington D.C., and we see Carly, Sam, Wheelie, Brains, and Colonel Lennox. Sam explains that after Laserbeak got away, he ran home and grabbed Carly and Bumblebee and they came straight there. Wheelie says he thinks it was the Decepticons. Sam says he knows it was the Decepticons. Someone named Wang said that Sam needed to warn Colonel Lennox and everyone. Apparently Wang also mentioned the moon. Carly asks why Decepticons would bother to kill humans, and Colonel Lennox says they're probably after what they just found. Then, a lady enters and starts complaining that this is a security breach of the highest order. Sam tells the lady to show some respect. Colonel Lennox introduces Sam to the lady, who is U.S. Intelligence Director Mearing. Director Mearing says she knows who Sam is and personally denied his application to work for N.E.S.T. because the squad is for veterans, not boys who once owned special cars. Carly says that's not fair and calls Director Mearing "Ma'am", and she doesn't like that.
- Page 30: The door opens to reveal Ironhide and Ratchet. Voice over by Megatron(?) presumably about how he could be jealous, after all Autobots have friends, but he takes solace that only friends keep secrets from one another. Ironhide points out Sentinel Prime to Sam. Optimus opens his chest to revive Sentinel with the Matrix. "Sentinel Prime.. we bid you return." He awakes.
- Pages 31-36 are missing.
- Page 37: We're at Sam's apartment with Agent Simmons, Bumblebee, and others. Carly walks in and Simmons asks who that is. Sam says he didn't hear her come in, and Carly says she came in through the kitchen. She asks what's going on and asks if he forgot. Carly tells Sam that it's Saturday and they were supposed to be at Dylan's party. She says she told him about it and it's for her job, the one that pays the bills. She said Sam told her she was done with this, that after what happened back at his school he was done with all the "life-and-death" stuff. She says the Autobots will take care of it and that's what they're here for, Sam is just in the way. That's what Director Mearing said. Sam says he didn't ask to be attacked by a Decepticon and this isn't what he wanted. Carly doesn't believe him and tells him good luck and she has to go. She rips the foot off the stuffed bunny. Simmons tells Sam he's better off this way and that "the warrior's path is a solitary one."
- Page 38: At night, we see Atlantic City. We see Agent Simmons, Sam, and someone else. Simmons says, "Nothing like going to a gig with Autobot backup." He talks about how Brains came up with three U.S.S.R. cosmonauts who made some interesting claims back in 1972. A former NSA member tracked him down. They walk into a bar and Simmons talks to one of the guys and tells him he knows who he is. Simmons says he was supposed to go to the dark side of the moon, then the whole program got shut down and asks him why. Suddenly, a bunch of guns are pulled at them.
- Page 39: The Russian cosmonaunt tells them they don't fear them just because they work for aliens. Sam says they don't work for the aliens, or at least not the bad ones. Brains is there with Sam and the others, and he starts speaking Russian and says they're the good guys and says they can ask him anything about the universe. The Russian guy said he dreamed of meeting life from another planet and didn't expect it to be so adorable. Sam asks the Russian guy if he knows what's up there on the moon. The Russian guy says the Russians were first to send cameras and saw hundreds of pillars on the moon. Sam says they found five of them, so the Decepticons must have the others. He wonders why they left Sentinel Prime since he's the only one that can use them. He then realizes something.
- Page 40: We see a lady who is apparently Director Mearing walking in a parking lot talking on the phone. It's Sam on the line and he tells her it's a trap and she asks who it is. Sam says they need Sentinel Prime to run the space bridge. Director Mearing says, "Mr. Witwicky, I thought I was clear..." Sam continues and tells her the Decepticons wanted them to find Sentinel Prime because only Optimus Prime could revive him. They need Sentinel Prime to run the space bridge, so they're escorting him back now. We see Sam in Bumblebee and there are other Autobots in vehicle mode there, including Sideswipe, Mirage, and Sentinel Prime (in fire truck mode). Director Mearing tells Sam that they have his space bridge and that it's safe. Sam tells her she has five pillars and they have hundreds. They're going to be coming for Sentinel Prime. They approach a bunch of Chevy Suburban SUV police cars.
- Page 41: One of them transforms into a Decepticon Dread and attacks a car, pulling Agent Simmons out of the rooftop. The Dread on top of the car being driven by Simmons' assistant then gets hit by an overpass sign.
- Page 42: Sam driving Bumblebee is being chased by the Dreads. Sam tells Sideswipe to tell Sentinel Prime to get out of there and for them to cover Sentinel. Simmons' assistant pulls up and runs over Simmons' leg. Sideswipe tells Sentinel to get out of there and head to base. Sentinel tells them to be safe. Sideswipe says "Safe isn't in our vocabulary, sir. You with me, Mirage?" Mirage replies, "Sideswipe -- there's nowhere else I'd be." Both are in Stealth Force mode using Mech tech weapons that appear from the vehicle.
- Pages 43-45 are missing.
- Page 46: Sentinel Prime blasts Ironhide in the face and says, "I have always been the key."
- Page 47: Ironhide dying says, "Sentinel... w-why?" and Sentinel Prime says, "I am sorry, my Autobot brothers." Sam, Simmons, Bumblebee, Skids, and others stand watching in shock. Optimus Prime's narration says that long ago on Cybertron, his mentor Sentinel Prime made a last-ditch effort to end the war between Autobots and Decepticons. Sentinel Prime's ship was blown out of the sky, and the war has continued ever since. Optimus Prime spent his life believing he was dead, and then he found him. He believed his fondest dream had come true, but he was wrong.
- Pages 48-58 are missing. Somewhere in the middle of that, we have this scene: we see some human shooting a cannon at what appears to be Sentinel Prime. He tells Optimus to run for it, and we see Bumblebee standing next to the human. Optimus Prime's narration says, "Only thanks to my friends do I survive. But the dream has truly become a nightmare." We see what appears to be an evil Sentinel Prime punching Optimus Prime and Sentinel Prime says, "Let the humans serve us, or perish!" Bumblebee and the human are still there and Optimus is on the ground and says he told them to leave. Bumblebee and the human said they're not leaving and the human said, "since when did I ever listen to you, Prime?" The human asks what they should do next as he fires at what appear to be other Transformers and Optimus Prime's narration says he doesn't know. It looks like half of Optimus Prime's face is missing and only one eye is visible. His narration says, "But my friends count on me. Fate has placed me here... and fate... fate rarely calls upon us at a moment of our choosing."