On a seemingly normal day, SpongeBob and Squidward are on their way to work when huge asteroids started raining down on Bikini Bottom. A huge drop of glob falls on Squidward, causing the top part of his face to turn orange. He then becomes a cyclops of sorts. He chases SpongeBob around the perimeter of a house until Patrick intervenes. Jimmy Neutron then arrives to take them to the Volcano Island. Soon, the gooey creatures spawning from the asteroids start taking over Bikini Bottom.
SpongeBob, Patrick and Jimmy arrives at the Mawgu Lair, where they meet Danny Phantom and Tak and the new "Evil Syndicate" composed of Technus, Beautiful Gorgeous, Tlaloc, and Plankton. Zim and Dib then arrive, with Zim joining the heroes, and Dib joining the Syndicate. They make a plan to stop the gooey creatures, identified as Morphoids when the Wise Old Crab arrives to inform them about the technology in the lair. Jimmy is able to figure it out, and fits everyone with weapons fitting their personality: Jimmy received a helmet and a tennis racket, SpongeBob got a bubble blower, Danny received a device that allowed him to partly clone himself, Tak was given a staff, and Zim received a plunger. Meanwhile, on the evil side, Technus received an arm blaster, Plankton was given a hammer that allowed him to grow, Tlaloc received a pouch of magic potions, Dib was given a gun-like balloon launcher, and Beautiful Gorgeous received a heart-shaped megaphone.
They travel through Bikini Bottom, and they meet Bubble Bass, who grows gigantic and becomes a Morphoid after eating his last patty which had just been covered in goo. The group battles an army of Morphoids and manage to free Gary, Squidward and Patrick from the goo. They defeat the corrupted Bubble Bass by feeding him Krabby Patties, causing him to vomit a large amount of goo onto SpongeBob. Back at the lair, SpongeBob suddenly speaks in evil voice after getting washed of the goo before quickly snapping back to normal. Shortly after, the Wise Old Crab informs them that a huge ship called the "Vessel of Portentia" is hidden in the Mawgu Lair, and requires four special components to power it up.
The group moves to is Zim's town, where GIR was playing with a taco that happened to be the first component of the Vessel of Portentia. GIR becomes mutated by the goo before giving, picks up the component, and runs away. The heroes and the Evil Syndicate manage to free Ms. Bitters, Gaz, and Professor Membrane before facing the corrupted GIR, who has taken over the security system of Zim's house. He soon tires out of attacking the heroes and is then beat up out of being possessed. The house drops some goo, which lands on SpongeBob. SpongeBob celebrates getting the component, but interrupts himself in the evil voice that threatens it will be "smugglering" the planet. The group discovers that the absorption of goo in SpongeBob's body has created a wavelength enabling the leader of the Morphoids to talk through him. SpongeBob snaps out of it when he smells a Krabby Patty Patrick was holding.
They then venture to Amity Park, they find that Morphoid asteroids rain on the town, freeing the Ghost Dog in the process. Goo falls on its head, resulting in him going on a mutated rampage through town. After freeing Dash, Tucker, and Jazz, they fight the Ghost Dog at Axion Labs, where Ghost Dog crashes into the wall, and goo flies off onto SpongeBob. They gain another piece of the Vessel. Back at the lair, SpongeBob is once again possessed the Morphoid supreme leader, who reveals himself to be Globulous Maximus. Technus flicks SpongeBob's nose to snap him out of the trance when the Krabby Patty smell fails. SpongeBob tells his group that he saw Globulous Maximus, who is the ruler of the Morphoids and will bring "doom, gloom, and evil."
Heading to Retroville, the group discovers that the goo has turned Jimmy's girl-eating plant into a monstrous giant, preparing to eat Cindy whole. After defeating several more Morphoids and freeing Carl, Cindy, and Sheen, they fight the girl-eating plant at the mall. After defeating the plant, SpongeBob gets covered by a glob of goo again. The third piece of the Vessel is retrieved, and SpongeBob states that Globulous Maximus is only a few light-years away from Earth, preparing to send more gigantic Morphoids to destroy it.
Finally, they go to Pupununu Village and find the fourth and final component of the Vessel of Portentia covered in goo after freeing Jibolba and Jeera. SpongeBob pokes the goo to try and free the component, and gets covered in goo. He grabs the component and races to the Mawgu Lair. At the Mawgu Lair, the evil voice of Globulous Maximus informs SpongeBob that he likes him and plans to become him.
The team quickly inserts the pieces of the Vessel of Portentia and then speeds toward space, where they confront and defeat Globulous Maximus, who is a large asteroid himself with floating arms and a primary eye. After Globulous is defeated, the Evil Syndicate betrays the rest of the group, taking over the Vessel of Portentia and ejecting the heroes from the robot. Globulous Maximus then opens up to the heroes, where he reveals that he was created at the beginning of the universe, the Big Sneeze, thus making him a huge orange booger. SpongeBob then asks why he was destroying worlds, with Globulous replying that he was distasteful of his form and thus took out his anger on others. SpongeBob then tells him to embrace who he is, and they throw Krabby Patties in his mouth to make him feel better. The group then wonders how they will stop the Evil Syndicate from taking over the Earth. Globulous states that he has an idea, as he morphs into a huge, orange, and cycloptic version of SpongeBob. Depending on the player's actions, one of two endings will occur.
Good Ending: Achieved by simply defeating the final boss, Globulous and the heroes manage to defeat the Vessel of Portentia on the moon, it explodes in space, leaving the villains floating around space. Globulous returns the heroes to Volcano Island, and says that he will right the wrongs in the universe by taking the moniker "SpongeGlob." The heroes bid him farewell, and SpongeGlob blasts off into space. Meanwhile, SpongeBob sneezes, and the goo finally exits from his body through his many holes. Patrick compares this moment to the beginning of the universe where SpongeGlob was born, while the Wise Old Crab then summons a typical "The End" sign.
Bad Ending: If the second player take control of the Vessel of Portentia on a save file that has not already been completed and defeat the first player. The villains are shown to have captured Globulous in a giant glass jar, with the credits rolling immediately afterwards.
Jimmy Neutron, Danny Phantom, SpongeBob SquarePants, and Patrick Star were the only characters that appeared in all four games, while Danny and SpongeBob were the only characters playable in all four games.
The beta cover was completely different than it's final cover.
This was the second game in the series since Nicktoons Unite where Patrick Star is not a playable character.
This was the third Nicktoons crossover game to feature Plankton.
Exclusively on the Wii version, if the player exits the hub or the loading is not complete, the game file will become corrupted.
Plankton is the only original syndicate member from the first game.
This was the only Nicktoons Unite! game where SpongeBob does not use his karate gear as his weapon.
Although, his glove can be seen as a power-up.
This was the second time in a row that GIR appears in a Nicktoons Unite sequel.
The goo in the game is similar to the Nickelodeon logo goo.
This was the last SpongeBob SquarePants video game released for the PlayStation 2, as the PlayStation 2 was discontinued in 2013.
In the Bikini Bottom levels, Bubble Bass is heading towards the Krusty Krab, at the end of the first level SpongeBob and Beautiful Gorgeous are seen at the Chum Bucket, it is unknown why they did not just cross the street to get to the Krusty Krab.
All of the playable characters have nearly-identical contextual dialogue, often repeating lines word-by-word with little variation.
In the first Bikini Bottom level, some of the boats say "Y2K Shell."
Running gag: Goo falls on SpongeBob.
The box art and disc art use the 2008 SpongeBob logo, but the game's title screen uses the old one.
This is the only PlayStation 2 game to use the 2008 SpongeBob logo.
The PlayStation 2 and Wii versions have the same gameplay, while the Nintendo DS version has its own gameplay style.
Globs of Doom is the only Nicktoons Unite! game not to feature any The Fairly OddParents characters (Therefore making this unknown if Timmy Turner, along with Cosmo and Wanda learned about this game event.)
All previous games in the Nicktoons Unite series were developed by Blue Tongue Entertainment for the console versions. Due to Blue Tongue Entertainment being busy working on De Blob for the Wii at the time, THQ hired Incinerator Studios to handle development on this game.
This game is the only Nicktoons game developed by them.
In the Bikini Bottom hub, there is a strange texture around and on top of Patrick's home. The texture seems to come from Patrick's model.
The game continually switches between day and night in some of the levels. When SpongeBob and Beautiful Gorgeous travel to Bikini Bottom, it was day time. But when Jimmy and Plankton were at the Bikini Bottom Dump it was night.
In the game, characters cannot run or jump in goo, but in the first Bikini Bottom level, at least 1 citizen runs through the goo.
In the second Amity Park level, there is a glitch from when the player pulls the three Switches the fan won't work and the player will get stuck on the level.
Many errors are present in "Dump City":
Mr. Krabs' mattress is seen even though he supposedly took it back home after "The Lost Mattress." Although this could have been someone else's mattress, it is unlikely because it had money in it and most people, other than Mr. Krabs, don't put their money in a mattress.
Mr. Krabs and Plankton's childhood hangout spot from the episode "Friend or Foe" can be visited in this level. However, it has a hole at the top of it, this is an error because in the real version of the story neither Plankton nor Mr. Krabs were shot out of the roof. When the player(s) go(es) inside it looks different than from the episode.
After getting off the bus, the characters appear right before the bus does to let them off.
In the Theater, after entering the bathroom and enter one of the stalls a fish runs out and runs off to the wall, he is just running in place at the wall.
During the cut scene before the second Bikini Bottom level, Plankton says that the Chum Bucket is in danger, but, the Chum Bucket is not seen in the next level.
In the first Amity Park level, when the player(s) go to the top of Casper High and look at the baseball field, the giant morphoid monster that appears later is not there.
In the first Bikini Bottom level, after the player(s) pass(es) the 3 houses, there is a sign that says "Bikini Bottom 50 miles." This is inaccurate because SpongeBob, Patrick, and Squidward live in Bikini Bottom.
In the first two Bikini Bottom levels, in the gameplay, the buses don't have the "periscope."
In the second Bikini Bottom level, the Reef Cinema is in town, but in the series, it has a path leading to the cinema, which separates it from the town.
In the reef cinema, Squidward is trapped in glob. However, in the first cut scene, Squidward got turned into a glob monster.
In the first cutscene, Patrick was seen SpongeBob in the Mawgu Lair, but however in the first level he was shown in his rock. In the following level he was trapped in glob in the reef cinema and in the last level, he's shown on a boulder rolling down at Pupununu when SpongeBob and Zim were getting the last part of Vessel of Portentia.
In the first Amity Park level, when leaving the park, the sign is shown, but when the player looks back, the letters are missing from the sign.
On Amazon.com, the product description of this game says that Professor Calamitous is a playable character, but he is not seen or mentioned in the game.
There are also some out of bounds glitches in some areas.
In the episode "Prehibernation Week," SpongeBob slide down on his tongue on Sand Mountain, in some parts of the game, there's is a slide for SpongeBob and the other Nicktoons when they slide down to get to their home words.
The food track from "Friend or Foe" can be seen in the second level.