Last time, Team Sonic met Mighton and Bolts, two heroic robots from an automaton-populated city in the sky named Morristown who'd crash-landed near Hedgehog Village. Unfortunately, the robot duo were convinced that the protectors of the Village were remorseless destroyers of their kind due to arriving in the middle of another of the heroes' fights with Eggman and his Badniks and attacked the quintet, leaving afterwards with the evil scientist; Eggman attempted to convince them that he was a victim while learning of Morristown and deciding he wanted it for himself. However, Mighton and Bolts would realize Eggman was no friend of theirs and be subsequently captured for questioning. After Team Sonic mounted a successful rescue, the duo apologized for the misunderstanding and left for home on good terms with them, but the heroes would then be ambushed, with Tails getting shot down by a laser blast. This tense scene is where we rejoin Team Sonic, with the other members still surrounding their motionless teammate outside his workshop. For several worrying seconds, the four wait for a response from Tails. Something. Anything. And to their relief, Tails' eyes flutter open and, while sitting up, he reveals that he got a lucky break. He pulls out his now-charred copy of Wolf Sidekick's "Always Settle for Second-Best" book and tells them it was in his strap when he was hit; it shielded him from the laser's full brunt, leaving him stunned, but otherwise unharmed.
Tails may be alright, but Team Sonic must still deal with the ambushers that put them in this mess. They once again assume fighting stances as their attackers emerge from the bushes and reveal their identities; they're the Cubot prototypes Sonic and Tails befriended, carrying blasters and cattle prods with them. As the former Eggman robots continue to attack them, Knuckles is puzzled over their sudden change of heart; usually, they're nice, but all of a sudden, they're out for blood. Sonic orders his team not to hurt them... and then presses one's self-destruct button on his head by accident while holding him back. This gives Tails an idea: subdue the prototypes using their self-destruct buttons. After this, the team easily dispatches them. Tails decides that he needs to put them back together so he can deduce the reason behind their newfound hostility (this, of course, gives Sticks cause for concern).
At Eggman's lair, Eggman is recovering from his humiliating loss last episode with a bubble bath, but it doesn't soothe his anger over failing to get the location of Morristown from Mighton and Bolts. But ever his loyal minions, Orbot and Cubot are there to reassure him, and surprisingly, instead of letting loose his usual putdowns, he genuinely appreciates their words. With their help, a reinvigorated Eggman decides that he doesn't need Mighton and Bolts, because as long as he has his robots, nothing's impossible! ...And that turns out to be a poorly-timed declaration, because a strange signal causes Orbot and Cubot to abruptly change in behavior and float out of the room, leaving Eggman upset and demanding to be scrubbed. But it's not just them— almost every robot of Eggman's suddenly exits his lair without his input and heads toward Seaside Island. As you can guess, this is a recipe for disaster.
Inside Tails' Workshop, Sonic stands by as Tails scans the fixed Cubot prototypes, and it turns out they were infected by the same malware that was on Mighton and Bolts' ship. Fortunately, he's removed it from their systems, so it shouldn't happen again. At that moment, Amy calls them on their Communicators. It's an emergency, as the rest of the team is dealing with a sudden Eggman robot invasion in the Village Center. In response, Tails says those forbidden words— "things can't get any worse". And they do, as the Cubot prototypes are reactivated by a signal, again infected with the malware. Sonic and Tails decide they don't have time for this; their friends need help, and the Village needs saving. Again. They shut the prototypes in, and Sonic tells a nearby Leroy the Turtle, out doing his usual mail delivery, to watch the door and ensure the prototypes don't escape before the two leave... and Leroy does nothing as the prototypes break down the door except continue on with his day, citing it's "not my problem".
In the Village Center, Team Sonic fights hard to stop the robot assault as Soar the Eagle commentates on it all, berating society for not lending a helping hand as he himself doesn't lend a hand to Mrs. Vandersnout as she struggles to take her purse back from a Crab Bot; fortunately, Sonic takes care of the issue. Soon, Orbot and Cubot arrive piloting the Octopus Bot, and Sonic, while dodging ink projectiles, is annoyed that despite them tattling on Eggman's scheme an hour ago, they're doing his dirty work for him now, but Orbot and Cubot say Eggman isn't giving them their orders. Regardless, Sonic quickly destroys Octopus Bot, with the two rogue minions escaping unharmed. Meanwhile, Tails scans the robots and discovers the malware signals they've been encountering are all around him. It seems to be a full-on robot takeover. Looks like Sticks was on to something about the robo-apocalypse. And people call her crazy.
A panicked Mayor Fink pleads with Sonic and Tails to do something to put an end to this robot riot and save their town (even if it's for his own political reasons). Tails says he's found out that the signal affecting the robots is coming from Morristown and that he downloaded the coordinates of the city in the clouds from Mighton and Bolts' ship; if they can get there, then they can shut down the signal at its source. Mayor Fink, despite having no idea what he just said, tells them they might as well go for it anyway. Sonic asks Knuckles, Amy, and Sticks if they can stay behind and hold down the fort in the Village Center while he and Tails deal with the signal, and the trio are confident that they can handle the army by themselves. As such, Sonic and Tails are free to go to Morristown (though Sonic still thinks the place needs a better name).
Soon enough, the duo has launched Tails' Plane and are headed towards Morristown, but they find themselves in the middle of a dogfight with the city's sentries, all piloted by robots. With some fancy flying, some good aim, and a Spin Attack from Sonic, they're able to take the ships down (don't worry, the robot pilots eject safely towards Morristown); one that Tails outmaneuvers and blasts from behind lands in the canyon below. Tails lands his plane and gets out to run towards it, leaving Sonic confused as to why he's suddenly abandoning his pride and joy; Tails says that his plane has no chance of making it through if there's more sentries, so it's time for plan C (plan B involves bowling shoes filled with pudding, but they can't find those on such short notice). Sonic is willing to join Tails in this reckless decision, and the two enter the ship.
Back on the ground, in the Village Center, Knuckles, Amy, and Sticks are holding back the relentless robot horde as they promised (with Knux eating pudding from a bowling shoe), and Amy is certain that eventually their might will win out. Things seem to be turning even more in their favor when Team Sonic ally and former Eggman robot FriendBot enters the scene and Amy asks for his help, though a distrustful Sticks keeps her battle stance. She's right to be on guard; FriendBot's been infected with the malware, too, and is fully intent on destroying them. As Amy and Sticks run and hide from his attacks behind an overturned table at Meh Burger, Amy hopes that wherever he is, Sonic is kicking butt.
But Sonic isn't kicking butt— rather, he's sitting on his own as he plays with his seat inside the commandeered sentry ship, Tails diligently working to get it online. He succeeds, and they fly towards Morristown without any further incident, as the sentries believe them to be one of their own. When they get close to Morristown, the ship enters an auto-docking sequence and flies in by itself, and Sonic and Tails are, at a distance, awed by the city's beauty, but as they look closer, their awe turns to shock; the city's not quite looking like the utopia Mighton and Bolts described— more like a horrible trainwreck. There's ruined buildings and debris everywhere. The atmosphere is cold and gray. The streets are empty. Once the ship lands, Sonic and Tails step out to get a better picture of the formerly-pristine Morristown, and as the episode ends on another cliffhanger (again, to the chagrin of Knuckles, who doesn't appreciate "the nerve of these writers"), the duo are left wondering what happened to the city in the clouds.
This episode contains examples of:
- Bait-and-Switch Comment: As Tails is about to enter a downed sentry ship, Sonic tells him he's "being irresponsible and totally reckless", seemingly attempting to dissuade him from going through with it, but when asked by Tails what his point is, he finishes with "And wait for me!" before entering the ship along with him.
- Continuity Nod: During their dogfight with Morristown sentries, Tails refers to himself and Sonic by their codenames previously used in Boom's pilot episode, "The Sidekick": Yellow Sky and Blue Leader, respectively; not really necessary, though, as Sonic's right behind him. Old habits?
- Don't Try This at Home: Said verbatim to the audience by Sonic before he jumps from Tails' Plane in mid-flight to Spin Attack a Morristown sentry. Yeah, probably not the best idea in real life, that.
- Let's Split Up, Gang: After Tails finds out the source of the malware signals causing robots to go berserk is coming from Morristown, Team Sonic decides it's best to split up for the moment; Sonic and Tails head to Morristown to shut down the source while Knuckles, Amy, and Sticks remain behind to defend Hedgehog Village, which is still under attack from the robots. From here, the show constantly switches between the two sub-teams until Team Sonic reunites midway through Part Four.
- Old School Dogfight: Sonic and Tails end up in aerial combat when Tails' Plane attracts the attention of Morristown's sentry ships.
- Pocket Protector: Part One ended with Tails taking a direct hit from a laser, but in this part, it's revealed he survives it unharmed thanks to a book he carried in his strap (somehow).
- Story Arc: This episode is part two of an overarching plotline taking place over the course of four episodes.