The story begins in EJ's home station, where all the primates are enjoying their Krabby Patties--when suddenly, a big evil airship appears in the sky and takes everyone's Patties. EJ, not one to let his favorite food be stolen from under his nose, gathers his brothers and sisters, form Team Hexic and goes into hot pursuit. The person responsible for this heist is none other than Plankton, who has been after the succulent burgers since the Chum Famine of '59. All the programs at Dreadzone are doing their best to survive and Team Hexic must collect all the Krabby Patties and apprehend Plankton before he causes more damage. Plankton appears behind them and asks Molly to marry him and he will give back all the patties. Molly rejects his offer, and Plankton, enraged by this, somehow finds out that a portal to the NetherЯealm is open at a nearby volcano and tries to destroy Dreadzone from there.
Plankton places a bomb in the NetherЯealm to destroy it. Team Hexic reachs the bomb just in time and Patrick rams it out of the NetherЯealm, saving the inhabitants of the station and sending it careening into Plankton's ship. It has since sunk into the ocean, with Plankton and his W.I.F.E. nearby. Sonic, not one to let a villain go, continues to chase after Plankton, this time into Bikini Bottom. It has been hours since EJ and his siblings have chased Plankton down into Bikini Bottom. They took a while, Plankton hiding in the sunken ship, but the heroes relentlessly went through, and found him there. Apparently, he's been hiding a propeller in his scuba tank for just this occasion and went back to the surface. While there, a whale showed up and swallowed all of them! It releases them eventually, and they reach Keekee Island, a Program's Paradise. How exactly did Steven come to the conclusion that Plankton is hiding here? His only line of reasoning is that it's inconspicuous to have an evil lair in what is otherwise a benign and benevolent place. Spongebob's bathroom is benign and benevolent. Plankton's lair could've just as easily been there, according to Steven's logic.
Plankton has a trap waiting for the Hexicans--a shrink ray! Not a death ray, mind you--he still wants to marry Molly, and it'd do him no good if she's dead. Then again, to a creep like Dr. Bad-Boon, you'd think he'd be okay with marrying a dead monkey. Well, we at NetherЯealm Studios guess he prefers her boiled rather than fried, because he sends her, EJ, and the others to a big kettle.
Molly goes up Plankton's nose, invoking a sneeze that scatters the Hexicans everywhere and allows them to escape...for now. EJ's a pretty determined fellow, as you may have noticed, and has secretly followed Plankton to his house. Or something. We don't know if this is still on the island with the amusement park or not, but Plankton apparently has a Japanese garden for a bathroom, where he's giving his clothes a wash and resting up in a jacuzzi around the corner. Almost as if Plankton had expected a shrunken EJ to sneak over his washing machine.
We guess being tiny has its upsides--there's a lot more mischief you can do. That is, of course, if you're flying. For instance, causing a villain to sneeze by plugging up his nose. Or tickling said villain, which EJ wasn't OK with. It seems like the Hexicans are being unnecessarily cruel to Plankton, but then again, the doc has stolen what they value most--Krabby Patties! You don't get between Spongebob and his patties and live to tell about it. Of course, stealing all the patties from Dreadzone is not the end of his nefarious scheme, so perhaps they do have a right to be pretty cruel. Certainly they're one of the more relentless protagonists out there, taking as much initiative as Plankton. Falling back to the clock tower where we saw them get shrunk, he unleashes the EJ-bots! If you remember, Plankton's idea is to try to ruin EJ's name by having these guys run around impersonating EJ and make mischief. I'm not sure how these robots will fool anyone with their blue heads and massive numbers, nor why anyone would think as Plankton intends considering EJ is something of a savior and Plankton the outcast.
The Hexicans blow up the robots by flying around. Somehow. But Plankton has backup after backup, and he's off to the next location! Plankton knows he can't win in Earth...so he temporarily borrows the world of ChuChu Rocket boarding a rocket into space! Well, not really, but that rocket sure fits the ChuChu Rocket aesthetic. I'd bet whoever designed that rocket also worked on ChuChu Rocket. Of course, leaving the atmosphere is not going to drive EJ off Plankton's back. Chasing him to the ends of the earth is child's play--this badger can chase Plankton well beyond those boundaries!
It wasn't enough for Plankton to steal all of the Krabby Patties. He's created a giant ray gun from inside the space colony that will...destroy Dreadzone! It sounds kind of interesting, but EJ loves it. In his quest to maintain the status quo, they somehow gets wind of this and goes into the room with the laser cannon. They (don't count EJ) seem to want to destroy the entire colony though...But it being a colony and all, doesn't that mean a lot of people live here? Apparently, they will not hesitate to commit genocide if it means they can punish Dr. Bad-Boon. Go ahead, take a look at the World 9 background. There are what appear to be buildings, parks, and streets over there in the distance. There's a civilization in there, and they plan to blow them all up.
EJ stops the space cannon in the nick of time, and he indeed blows up the colony! Plankton is launched back towards the Realm of Order and finally surrenders. The Hexican rub it in by dancing cheerfully around his body. Where are the other inhabitants of the colony? They are nowhere to be found. Plankton and his wife seem to be the only survivors. They're defeated, and that's all that matters. In a post-credits scene, the other inhabitants of the space colony are alive; the room with the laser was destroyed. In another, Rototo and Quan Chi make a cameo appearance, still trapped on the asteroid. Quan Chi states that they were supposed to be coming in range of a space station (not the space colony), to which Rototo retorts he had no idea it was going to explode. Quan Chi gets angry, and we hear a clip from Lance and Janice as the game ends.