The adventure resumes in the same spot where it left off: Shadow has wreaked havoc on Sonic and his friends because Eggman has suckered him into fighting them so he can motion capture the former's moves for his video game, and he's on the verge of finishing Sonic off. Shadow asks his seemingly doomed rival for his last words; Sonic answers with a nonsensical phrase that actually manages to confuse Shadow long enough for the Blue Blur to hit him with a sudden attack. And so the battle between old rivals begins anew, with the two constantly trading punches, kicks, Spin Attacks, and insults. Eggman, who's still there watching with his Spy Bots still recording the footage, couldn't be happier, overjoyed at the thought of putting Shadow's moves on his character skin. As the fight grows more intense, his excitement becomes too much, and he decides he can't wait to program these moves into the game, so he leaves for his lair at once, calling his Spy Bots to join him.
Eggman picked a bad time to leave, however, because as Sonic and Shadow's battle heads into Meh Burger, Sonic finally decides to ask why Shadow's attacking him and his friends all of a sudden. Shadow explains that he must pay for his insults, and Sonic remembers the interview with Eggman at his shack earlier and tells Shadow that he never said anything offensive about him. Shadow begins to catch on that Eggman manipulated the footage of the interview to trick him into fighting Sonic, and needless to say, he's even less amused than he was previously. Shadow's definitely not about to let the doctor get away with making him look like an idiot, so he cuts round two short, speeding away from Sonic and out of the Village Center to enact his revenge.
Meanwhile, Eggman has arrived at his lair and is about to program in the footage when there's a sudden thudding noise outside. When Eggman checks the security cameras, he sees Shadow attempting to knock down the door with Spin Attacks. Orbot notes that while the lair's teleportation guard prevents him from getting in the easy way, the door won't hold forever. Shadow then comes up to the security camera and orders Eggman to open the door and accept his fate, and Eggman justifiably decides he's not doing that, telling Orbot and Cubot to distract Shadow while he uses the lair's pneumatic tubes to escape to the roof. Just after, Shadow finally breaks in and demands Eggman's location, only to hear Cubot pretend he has no idea who Eggman is. The distraction doesn't work for long, and as Eggman takes off in the Eggmobile, Shadow bursts through the roof in hot pursuit, leaving behind the decapitated but still-sentient heads of Orbot and Cubot. Ouch.
Eggman, having somehow lost Shadow for the time being (maybe he blinded him with another selfie off-screen out of desperation), heads over to Mombot and Morpho's house and bursts in, telling his "brother" all about the situation he's in. In response, Morpho suggests he use his Inter-dimensional Portal Creators to leave for another dimension, and Eggman decides he can throw Shadow off his trail even further by getting another Eggman to be beaten senseless in his place. After creating a portal to another dimension, Eggman suggests Morpho use his shapeshifting abilities to change into something inconspicuous quick to avoid being mistaken for him by Shadow before jumping in, seeing as Morpho was built in his image (well, that of an alternate-dimension Eggman, anyway). Morpho takes the advice, shapeshifting into a glass unicorn that Mombot lovingly places on a shelf.
So, what dimension did Eggman head off to? The one where Sonic never existed and Lord Eggman formerly ruled with an iron fist. At his lair, said evil genius is plotting his revenge against Sonic for foiling his plans when Eggman arrives and reveals that he knows who Sonic is, as well as explaining how he got access to this dimension. Shortly after, Eggman fizzles, and since both Eggmen are aware that two versions of the same person remaining in one dimension too long will cause a calamitous anomaly to befall the universe, Lord Eggman quickly exits for Eggman's dimension using one of the Portal Creators, all while Eggman remains behind with the other and laughs to himself, having escaped Shadow's wrath for now and free to plot.
Elsewhere, a battle-scarred Team Sonic is recovering from Shadow's relentless beating in Tails' Workshop, lamenting over the pain and bruises he dealt them that probably won't go away for a long time. Unfortunately, our heroes don't have long to rest and nurse their wounds, as Lord Eggman appears, sights Sonic, and almost immediately rushes to get payback on him with a laser sword he brought. Sonic manages to dodge his swings, though one does graze him. Before the skirmish can go any further, Shadow barrels in and mistakenly attacks Lord Eggman, as Eggman expected to happen, but Lord Eggman is quick to point out that he's not the Eggman Shadow's looking for and that the offending Eggman is in his dimension, creating a portal that Shadow jumps through. Sonic follows right after, telling his friends beforehand to make sure Lord Eggman doesn't go anywhere.
Sonic and Shadow are spat out of the portal and find themselves in the alternate-dimension Village Center. Shadow asks for Eggman's location, but the two are immediately tipped off (and knocked down) by a laser blast. Eggman's already there, and he's brought an old friend— Metal Sonic, now loaded with all of the data Eggman recorded for his video game, meaning Sonic's robotic copy knows the every move of Team Sonic and Shadow. The three duke it out, but Metal counters all of their attacks and dishes out his own, which gives even Shadow trouble. In the midst of the fight, Sonic attempts to coordinate a team attack with Shadow, but saying he takes orders from no one, Shadow coldly refuses to hear him out and punches him away. Probably not the best idea. As the fight rages on, Eggman gets annoyed that his foes haven't been defeated yet and decides to join in by firing a rocket launcher, the recoil of which knocks his Portal Creator off the Eggmobile and onto the ground; this creates a portal, and Sonic and Shadow tackle Metal into it, with a further-irritated Eggman on their tail.
Back at Tails' Workshop, Sonic's friends have tied up Lord Eggman when a portal appears, the other-dimensional battle bursting into their dimension and causing explosions and destruction throughout the landscape as it heads into the Village Center. Sonic's friends, with Lord Eggman in tow, arrive just in time to see Shadow get blasted into the Eggmobile by Metal, sending them both flying into a building and causing its debris to fall towards Tails. Fortunately, Amy's there to push him out of the way and then rally her friends to join the fight, despite their still-lingering injuries. Amy attempts to land the first blow on Metal with her hammer, but this only prompts him to make an imitation hammer with a metal beam and a medium-sized rock. Feeling offended that Metal's stealing her shtick, Amy tries to attack again, but is knocked down by Metal's hammer, and the rest of Sonic's teammates are smacked down by repeated Spin Attacks from the robot. It seems as though Metal might accomplish the previously-impossible goal of taking down the entire team, but before he can act further, Sonic, Tails, and Knuckles each grab one of his limbs with their Enerbeams. Despite this, he still charges a laser to fire at Amy, who's getting back on her feet and is wide open. Fortunately, her BFF Sticks has her back, finishing Metal off by driving her bō staff through his chest cavity just before he can let loose.
Metal is brought offline by the blow and Team Sonic cheers in rejoice over winning the hard-fought battle, but their worries are far from over, says Shadow as he reappears on a building. He elaborates by saying that he's no longer satisfied with just taking revenge on Eggman, and he's decided to extend that revenge to the entire universe. He reveals he's taken both Eggmen to a secret location, and Team Sonic looks over to find that Lord Eggman's restraints are still there, but he's nowhere to be seen. Tails warns him that leaving both Eggmen in their dimension for too long will cause an anomaly to wipe out the universe, and Shadow pretty much tells him he's right on the money— he wants the universe to be destroyed (and honestly, after somehow allowing himself to be tricked by Eggman and outmatched by Metal in the same day, it's kind of hard to blame the prideful hedgehog for wanting everything to burn). He then bids the quintet adieu for what he believes is the last time and teleports away as storm clouds roll in. The end of the world has been set in motion.
Team Sonic instantly realizes the pouring rain, lightning, and intense winds are signs of the anomaly, and they know they must act fast to undo it before the universe unravels, destroying them all. Tails mentions that the still-offline Metal has an Eggman homing beacon built in, and that repairing him will allow the fox to find the Eggmen's location. Sonic tells him to get on that quick as he and the others go searching the old-fashioned way in the meantime. And so, the team splits up— Tails frantically attempting to make repairs to Metal in his workshop, Sonic roaming the forest in Blue Force One, Sticks taking flight in Tails' Plane to look from above, and Knuckles and Amy swimming underwater in their wetsuits, all as the storm continues to rage and the universe slowly edges closer to utter destruction. Tails eventually manages to bring Metal back online, and he immediately flies off, his Eggman homing beacon guiding him to his creator. Tails attempts to follow, but can't keep up; he tells Sonic all of this via his Communicator, and in a stroke of luck, Sonic notices Metal fly by while he's searching in the canyon and goes on foot to follow him, Portal Creator in tow.
Metal leads Sonic to the cave Shadow was in, where Eggman and Lord Eggman are tied up. Sonic quickly unties them, tells Lord Eggman he needs to amscray to his home dimension, and kicks him into the portal he creates (but not before the two Eggmen say goodbye). The storm immediately disappears, and the universe is saved in the nick of time; back in the Village Center, the rest of Team Sonic can at last celebrate properly. As Sonic and Eggman exit the cave, Shadow reappears and says that while he's not thrilled about his plan being undone, he still must admit he's impressed that Sonic saved the universe. He then promises the hero once more that he'll be back on his terms before teleporting off. Despite the fact he played a part in nearly destroying the universe, Eggman is still happy, as he gets to finish his video game using the footage he gathered, but a repaired Orbot has some bad news: lightning struck his lair during the anomaly, erasing all of his footage. However, Eggman nonchalantly shrugs this off, deciding he can just try it again next season. And he'll have to, because this is where the second season of Sonic Boom comes to a close.
This episode provides examples of:
- Always Someone Better: Shadow proves to be this to the whole of Team Sonic, delivering a Curbstomp Battle to the likes of Tails, Knuckles, Amy and Sticks, before proceeding to defeat Sonic one on one.
- Happens to Shadow later in the episode, too. Once Metal Sonic arrives on the scene, it's not long before he's overpowering the likes of Sonic and Shadow combined. It takes almost everyone in Sonic's group attacking him at once for him to go down.
- Any Last Words?: With Sonic at his mercy, Shadow asks him for his last words. This backfires spectacularly when Sonic yells "Volcano wonder pants!" in response, confusing Shadow on how that statement doesn't make any sense and thus allowing the Blue Blur to blindside him.
- Apocalypse How: After deciding the entire universe must suffer his revenge, Shadow attempts to create a Class X-4 by deliberately leaving two versions of Eggman in the same dimension to cause a universe-destroying anomaly, and it very nearly happens before Team Sonic manages to stop it.
- Battlecry: Volcano Wonderpants!
- Breaking the Fourth Wall: At the end of the episode, Eggman shrugs off the loss of his video game data by saying "there's always next season".
- Don't Celebrate Just Yet: Team Sonic has somehow managed to defeat Metal Sonic, who fought and nearly overpowered them with their own moves, plus Shadow's, thanks to Eggman's motion-capture data that he collected over the day. They have good reason to cheer over their hard-earned victory... until Shadow himself, who'd disappeared while Sonic's friends joined the battle against Metal, returns to outright tell them they shouldn't be celebrating just yet. Why? Because he just hid Eggman and Lord Eggman in a place no one on-scene but him knows about, knowing that the two Eggmen being in the same dimension together for an extended period of time will ultimately cause an anomaly that will wipe out the universe if not rectified. Needless to say, Team Sonic still has work to do if they want to live to see another Seaside Island sunset.
- Losing Your Head: When Orbot and Cubot are left at Eggman's lair to distract Shadow while their boss makes a getaway, Shadow severely dismantles them and pops off their heads. They're still operational, though (justified, since they're robots).
- Stealth Insult:Shadow: You have the reflexes of a panther.
Sonic: ...is that an insult? I thought panthers were fast.
Shadow: Maybe compared to you.
- We Will Meet Again: Once again, Shadow promises that he'll return on his terms after his plot to destroy the universe falls through.