Locked out of participating in the investigation by Ness, Shulk turns to Snake Simmons for help. Snake, who has become a millionaire as a writer, and his aide ,Marth , help Shulk find out that the Soviets have taken photos of Decepticons removing hundreds of space bridge pillars out of the Ark even before Mario 11 had landed on the Moon. Shulk and Snake conclude that the Decepticons had left Phoenix Dark Pit behind on purpose, knowing that only he would be able to activate the space bridge, and only Mario could reactivate him. Shulk is able to warn the Smasher in time so they can protect Phoenix from a Decepticon attack and escort him back to the NEST headquarters.
Ness : Mr. Witwicky, I thought I made it clear to you that I did not want you calling this phone.
Shulk : Listen, the whole thing has been a set-up since the beginning! The Decepticons wanted Mario to find Phoenix because he was the only one who could revive him.
Ness : But we have the space bridge.
Shulk Witwicky: Ness , you have five pillars - I just learned that they have hundreds! You're doing exactly what they wanted you to do! What do you need me to say to you? The Decepticons are coming for Phoenix Dark Pit !
Aided by Lucario, Falco and Greninja, they began escorting Phoenix back to the NEST base. En route, they were attacked by the Dreads, (Hatchet, Crankcase and Crowbar)were sent to pursue the Smasher. After Crowbar disposed of Snake Simmons, Hatchet and Crankcase leaped to attack, only for the Smasher to break suddenly and deploy their Stealth Force mode. Hatchet was targeted by the Greninja, who embedded his anchored blades into the Decepticon's back, and corralled Hatchet into the firing line of Lucario and Falco. After Hatchet was pounded with Smasher ordnance, Greninja tossed the Decepticon into the oncoming side of the highway, where he slammed into a passing car and was destroyed and the remaining Dreads were soon confronted by the Smasher heavy-hitter,Bowser , who stopped them in their tracks with a head-on collision
Bowser: Is there a problem?
Falco: Whoa, we got us a little Mexican standoff!
Bowser: Weapons down!
Falco: And we'll let you escape with your dignity!
Faced with Bowser's heavy weapons and Falco, the Dreads seemingly capitulated by dropping their ranged weapons, but as soon as the Smasher followed suit, they deployed spiked spears to attack their enemies. His partner was initially successful in injuring Bowser, and Crankcase kicked Falco to the ground , The veteran Smasher caught a blaster tossed by Falco and used it to shoot Crowbar in the face, before pulling the spear out of his shoulder, impaling it into Crankcase's face, slamming the Decepticon into an abandoned car and kicking the wreckage into a nearby auto shop, which exploded.
Bowser: Decepticon punk!
Sheathing his blasters
Bowser: Class dismissed.
when they arrived back at base, however, Phoenix reveals that he had made a deal with Dark Pit, knowing that the Autobots could never win the war.
Shulk : [to Dylan] We gotta get Phoenix outta here, he is the key to all this...
Phoenix Dark Pit: Indeed I am! What you must realize my Smash brothers, is we were never going to win the war! For the sake of our planet's survival, a deal had to be made... with Dark Pit!
[blasts Bowser]
Dylan: GET BACK!
Bowser: Phoenix... what have you done?
Phoenix Dark Pit: [to Bowser] I hereby discharge you from duty!
[shoots Bowser again]
After killing Bowser and several NEST soldiers,Phoenix Dark Pit attacks NEST base
Ness: Phoenix, stop this! What's going on? What do you think you're doing?
Phoenix Dark Pit: I do not answer to the likes of you. Return what belongs to me!
Phoenix Dark Pit claims the remaining pillars and escapes.[Mario arrives at NEST]
Ness: Take a good look, Mario! This is all your fault!
[at the Master hands Memorial]
Metalface : Oh, my master, such a brilliant scheme! So when Phoenix left Cybertron, it was to defect!
Dark Pit: He was meant to rendezvous with me here on Earth, before fate waylaid us both. The only way to revive him: we needed Mario and his Matrix.
[blasts the Lincoln statue]
Metalface: Excellent strategy!
Igor: [chomping Lincoln's head] Mine! Mine!
Metalface: So, he is now your partner.
Dark Pit: He is my greatest triumph.
Metalface: So impressive!
The other Smasher track him down to Lightning kingdom, but before Mario can stop him, Phoenix activates a space bridge to the Moon.
Phoenix Dark Pit: Commencing transport.
[activates the pillars]
Mario: [arriving] Stop! No, no! NO, PHOENIX !
The portal allows Decepticon troops which had remained hidden under the Moon's surface to reach Earth, forcing the Smasher to retreat
In the meantime, Shulk is worried about Madison and searches for her. He finds her with her employer, Joshua loops , who reveals to Shulk that he not only arranged for Shulk to get a job with Acuretta, but is also a collaborator with the Decepticons. At their request, his father had used his influence to ensure that NASA would not conduct any more missions to the Moon. When Shulk and Madison attempt to flee, they discover Madison's car is a disguise for Orcos, who takes her captive. Joshua instructs Shulk to ask Mario about the Smashers' strategy, otherwise Madison will die. To ensure that Shulk will not try to warn the Smashers, he attaches a Decepticon disguised as a watch on Shulk's wrist, and it taps into his nervous system.
Meanwhile, Phoenix Dark Pit has given Mankind an ultimatum to exile the Smasher from Earth, since he is only trying to save Vestroia, or so he claims.
Phoenix Dark Pit: Defenders of Earth: we have come for your natural resources to rebuild our damaged planet. When we have transported all we need, we will leave your world in peace. For such peace to exist, you must immediately exile the Smasher rebels you have harbored. NON-negotiable! Renounce the rebels. We await your reply...
The US government promptly passes a bill to this effect. Before the Smasher leave Earth aboard their spaceship, the Xantium, Shulk asks Mario about his plan. Mario replies that there is no plan, and Mankind is on its own now.
Ness: These guys are the Wreckers (Ike,Marth,Lucina). They take care of the Xanthium. We don't let them off the base much, 'cause they're assholes.
Mario: What your leaders say is true: this was all my fault. I told them whom to trust. I was so wrong.
Shulk: That doesn't make it your fault, it just makes you human for a change.
Mario: Remember this: you may lose your faith in us, but never in yourselves.
Shulk: I need to know how you're going to fight back. I know there's a strategy, I know you're coming back with reinforcements, something. I know there's a plan. You can tell me, no other human will ever know.
Mario: There is no plan.
Shulk: If we just do what they want, how are we ever going to live with ourselves?
Mario: You are my friend Shulk, you always will be. But your leaders have spoken. From here the fight will be your own.
Toon Link: Shulk, don't let them take us!
Lucas: Don't let them exile us...
Toon Link: It's a Decepticon trap!
With all Smasher on board, the Xantium takes off,
[as the Smasher leave in the starship Xanthium]
Shulk: They're not coming back.
Joshua: We knew it. We just have to make sure they don't come back.
[signals Metalface, who blows up the Xanthium]
Metalface is promptly intercepted by who had waited in Earth's orbit. With the Xantium destroyed, the Decepticons believe the Smasher to be dead and let Shulk go.
Skyler: I still got my NEST friends out there. I'm a round 'em up, we'll find my sister and we're gonna bring this guy in.
Shulk: Why are you helping me?
Skyler: 'Cause that asshole killed my parents .