While the three are asleep inside the Rust Bucket, a bright light wakes the Tennysons up at 3:30 AM. They look outside and it is revealed to be a giant ship landing next to the Rust Bucket. The ship's pilot exits, and Ben prepares to go hero. However, the pilot shoots a diamond shard in front of Ben, revealing it to be Tetrax. Ben and Gwen are excited to see him since they haven't seen him since the last time, they took down SixSix. Tetrax says it's good to see them too and reveals that he "came as soon as he heard". Ben initially tries to apologize to him for destroying the hoverboard he gave him, but Tetrax says that he has actually come to Earth because he picked up the SDM signal from the Omnitrix. Ben still thinks it's merely another one of the Omnitrix's typical glitches. However, Max concludes that SDM stands for "Self-Destruct Mode". Tetrax says that it's natural for the Omnitrix to broadcast a signal when it begins its countdown. Ben realizes that the watch is going to destroy itself in a matter of time, and Tetrax adds to his fears when he says Ben will be destroyed along with it when it does.
Ben tries to think hard about how the SDM was activated in the first place. This leads him back to when they fought Animo at the reactor, but further condemns this as a mystery and tells Gwen that it doesn't really matter, assuming Tetrax can handle it. However, Tetrax reveals that he has no idea how to restabilize it, but Azmuth, the rumored creator of the Omnitrix, would be able to. Tetrax says that he can find Azmuth's DNA signature on the Omnitrix with the equipment in his ship, and they can use that to find him. After taking a look at the pattern repetition on the Omnitrix's hourglass dial (the pattern that indicates the countdown), he estimates that they have less than four days to deactivate the SDM before the clock reaches zero.
An alarm goes off from the lower level and Ben and Tetrax head down to search. Ben tries to transform into XLR8 to search for the intruder but transforms into Wildmutt instead and discovers that the intruder is Gwen, who says that she thought Ben needed backup. However, Wildmutt accidentally walks headfirst into a button and opens the hatch and venting the atmosphere into the vacuum of space. Wildmutt and Gwen are about to get sucked out into space, but Tetrax fires his shards at the airlock controls and closes the hatch as Wildmutt reverts back into Ben. Gwen explains herself, but Tetrax becomes concerned when he notices the Omnitrix's self-destruct countdown accelerating.
Later, Ben plays in Tetrax's hoverboard simulator and Gwen tries to have a conversation with Ben about this whole thing. Ben tells her that he's not worried about anything that could happen. Gwen reminds him that the life-threatening situation with the Omnitrix doesn't just affect him, stating that Max wouldn't want Ben to be vaporized (or whatever may happen if the watch doesn't get destabilized in time) and reminds him that Tetrax said that Azmuth would deactivate the Omnitrix, not fix it. Ben doesn't believe her, but Tetrax confirms, stating that having the Omnitrix deactivated would be his chance to return to a normal life. When Ben states that he can't go back to a normal life after everything he's been through. Tetrax tells Ben that his transformations speed up the countdown and tells him not to use it again to keep time on their side. The Omnitrix then releases another burst of energy like it did back at the mall, and this time, Ben goes flying and gets zapped hard.
Ben tries to activate the Omnitrix to transform into something else, but the Omnitrix is now timed out and has to recharge. Gwen grabs a pipe and fights off the aliens and Ben does as well. Tetrax and SixSix fight with each other when Tetrax sees the commotion. He climbs onto a hoverboard and comes to Ben and Gwen's aid and fights the prisoners. The female Chimera Sui Generis arrives and recognizes the Omnitrix, and she reveals that she is Azmuth, the creator they've been searching for. Gwen casts a spell that knocks out an alien prisoner and Ben asks Azmuth to fix the watch, and she says that she will if Ben frees her. A prisoner carries Ben off, but the Omnitrix discharges energy again this time knocks him unconscious. However, it did provide the kind of cover they all needed to escape. Gwen and Tetrax rush over to Ben, and he wakes up. Gluto flies over and opens the ship and the three manage to make it inside with the prisoners following. They all manage to knock the prisoners off of the ship but allow Azmuth to enter. Ben closes the ship and SixSix rides on the ship but is shot off and floats in outer space. Azmuth scans the Omnitrix, but reveals that she is actually Azmuth's assistant, Myaxx. The reason for the DNA signature from the Omnitrix leading them to her was because she erased his and put on her own because he never gave her the credit she deserved. Tetrax is furious when she also reveals that she can't stop the countdown on account of Azmuth not trusting her with the abort sequence and demands a reason not to shoot her back to Incarcecon. Myaxx says that she knows where Azmuth is: Xenon. The name frightens Tetrax and she explains the random energy bursts the Omnitrix keeps releasing: the watch is struggling to contain all the energy it's generating for the Big Bang, and they'll keep getting more powerful until the final detonation. Ben knows that he'll be destroyed if the watch explodes, but Myaxx says that he won't be the only one to die. Upon this, Tetrax reveals a secret that he kept from Ben regarding the truly dire stakes of their quest: If the Omnitrix is allowed to detonate, the explosion will cause an energy ripple that will literally rip apart the universe.
Vilgax attacks Ben and he runs off since there's nothing he can do with the Omnitrix in its current state. Ben tries to tell Vilgax that the Omnitrix is set to self-destruct, but Vilgax doesn't care. Meanwhile, Myaxx and Tetrax untether their ship from Vilgax's. After Ben fails to make a deal with Vilgax to help him find Azmuth and stop the countdown, he opens the hatch and Vilgax goes flying into space as the ship starts to enter Xenon's atmosphere. Gwen tries to fly it with little success and Ben arrives to help who saw remains of Gluto. Gwen tells him that Gluto sacrificed himself for her, which she refers to as "being totally unselfish. Something Ben wouldn't understand". Ben remarked his cousin that he is unselfish. Tetrax and Myaxx reenter the ship and Ben and Gwen stop the ship from crashing, but they fly into a rock pillar and crash anyway. The ship slides towards a canyon, but the two of them are able to stop it before it falls off. Tetrax and Myaxx arrive and the four ride hoverboards towards Azmuth's compound. They find it overrun by vines, which then are revealed to be wild Florauna and attack Gwen. The group shoot at the Florauna, but they keep coming. Gwen saves Ben from one, but it grabs her and drags her away instead. Seeing Gwen in serious danger, Ben has no choice but to turn into Four Arms, not caring about the dangers of the countdown despite Myaxx's warning. Four Arms chases after the Florauna attempting to rescue Gwen, but he is ensnared by countless vines, and it drags her underground and eats her. Once it gets away with Gwen, all the other Florauna stop attacking and leave. Four Arms breaks free and tries to rescue Gwen, but he cannot due to an impenetrable hatch closing behind it.
Finally, inside Azmuth's sanctum, Cannonbolt demands Azmuth to shut off the Omnitrix, but when he further refuses, Ben declares that if the universe is doomed anyway, he will not be denied the pleasure of vanquishing Azmuth first. Ben lands a critical blow and destroys his suit. Azmuth climbs out, revealing himself to be a Galvan, and Cannonbolt reverts back into Ben. Tetrax then demands Azmuth to stop the countdown, but states that the universe being destroyed is the best thing that could happen given his inability to see the good in people, revealing that the Omnitrix was intended to be a device for understanding all the beings of the universe, and people like Ben and Vilgax have caused it to be perceived as a weapon. Ben explains how he has occasionally used the omnitrix for personal gain but used it to protect those who cannot protect themselves for the most part. He finally manages to change his mind by telling him that to make a world worth saving, he can't just be a selfish jerk like Ben used to be himself. The lair begins to collapse and the four run outside, where Vilgax, SixSix, and many Mechadroids and Bioids are waiting for them.
Mechadroids and Bioids land and Vilgax sends SixSix to attack, too. Azmuth asks why Ben continues to defend the Omnitrix, and Ben says that it's because he thinks of people besides himself. He shoots some Bioids and two Mechadroids self-destruct from a spell cast by Gwen, who enters the battle with Gluto. Ben, in tears from seeing his cousin alive again, runs to embrace Gwen and she explains that Gluto regenerated from the particles left on her clothes from when he exploded back on the ship. When he reconstituted himself, he saved her from the wild Florauna. SixSix attacks them and the Mechadroids and Bioids march at them, but the group fights and destroys the robots while Tetrax battles SixSix. Ben's gun is destroyed, and he and Myaxx are surrounded by Bioids. Ben removes the Omnitrix's energy burst deflection device, where a massive energy blast destroys all of the Bioids and knocks Vilgax and SixSix away. Meanwhile, Azmuth deactivates the Omnitrix just before its countdown reaches zero through removing the dial. Giant Mechadroids climb to the group's position with Vilgax riding on one. Vilgax says that he will make Azmuth build him a better weapon when Ben says the Omnitrix is useless now. Azmuth grabs the Omnitrix dial while Tetrax destroys a Mechadroid.
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