Ratboy Genius

Ratboy Genius assembles his crew and departs through space.

Ratboy Genius talks to Fred about meeting up with him and the Caterpillar Minister. Sue spies on the Fish Legions, who are busy destroying a planet.

The Professor lectures about the forces of the universe, and gives exposition on the Fish Legion's ability to live off static electricity from stars and use that force as a planet-destroying weapon.

Little King John, suspicious of Sneezy's disappearances, follows him and discovers a secret portal room.

After travelling through the portal, Little King John finds the Caveman and plays a match of Knishball with him. He then marvels his surroundings, which had been mysteriously prepared for the flood.

Fred and George wait at the place they would meet up with Caterpillar Minister. Sue returns from a scouting mission and informs them of another planet's destruction. The Starship Genius crew (sans Clyde, The Professor, and The Hoo Hoos) also arrive at the meeting place, and Caterpillar Minister arrives shortly after.

Ratboy explains how the Fish Legions plan to unleash a single giant thunderbolt (The Final Charge) to wipe the galaxy of non-fish inhabitants, and how this can be prevented by using the Starship to redirect the energy into the Minecraft Dimension. Having seen this dimension in the future, he knows this has already been accomplished. The Starship will travel to the beginning of the Minecraft timeline and unleash most of its energy, creating the dimension. It will unleash the rest of the energy as water and cause The Great Deluge as a result. Mr. Bigarms and Very Tall Friend are later instructed by Ratboy to negotiate with Little King John in his dimension and look for an agent code-named "Sneezy".'

Mister Bigarms and Very Tall Friend visit Little King John's kingdom, as they are friends of Old Froggy.

Happyman and Green Monster set off on their Space Trike to Planet Fisheries.

Bigarms and Tall Friend reveal their reason for coming: to disclose information to Little King John and introduce the creator of the stronghold. The Ancient Artifact was a starship built by Ratboy Genius to absorb electricity from the Final Charge, teleport back in time, and create Little King John's world. To completely drain all the energy, the starship released enough water to completely flood John's world (an unfortunate side effect). Sneezy was a Galactic Friend named Buck Dodger, and had been codenamed as a spy to make sure Little King John found the Artifact and the portal device. Little King John contacts the person who sent them, and it is revealed to be Ratboy Genius. With reluctance, John must agree to Ratboy's terms if both universes are to be saved.

Happyman and Green Monster consult Young Mouthbottom for his permission to use his giant nets for the final battle.

Summer Solstice Baby meets up with Fisheater in order to ask for the help of him and his friends in the rally against Big Fish Boss.

Ratboy meets Green Flipper Friend, who teaches him how to use The Magic to become a goldfish.

Little King John and Sneezy are instructed by Ratboy to use a portal to meet with Caterpillar Minister. They find themselves at the entrance to The Minecraft Headquarters of the Galactic Friends, and ride hoverpads with Caterpillar Minister while discussing strategics and how to use "the Magic".

Ratboy uses his new goldfish-transforming powers to spy on the Fish Legions. Summer Solstice Baby also has fish-transforming powers and tags along.

Tensions are high as the time to fight draws near. Some fish invade the ship in a sudden attack.

Buck Dodger starts sneezing, a sign that The Final Charge is happening in Ratboy's dimension, and Little King John makes the dimensional connection needed to bring Bigarms and Tall Friend to the Starship, causing a storm to occur in his dimension. To maintain the power needed to keep the connection open, Caveman must hurl boulders at the portal's generator. Little King John is also teleported to the Starship, and returns when the storm clears. He tells Sneezy and Caveman of his brief visit to the Starship, but is unsure whether or not Ratboy and his friends are okay. Caterpillar Minister arrives on a hoverpad, congratulating him for saving an entire dimension, and informing him that he may soon too become a Galactic Friend. In the meantime, as a reward, the Minister gives him a hoverpad so he can leave his new kingdom at any time.

George calculates how to track the Final Charge's Thunderbolt. The Professor, Ratboy, and Solstice decide to use Mouthbottom's fish nets as guides for the upcoming Thunderbolt. Buck Dodger is given his code name and sent back in time to the Minecraft Dimension. The Fisheaters devour all fish surrounding the Star Ship. Big Fish Boss rallies the Fish Legions to swim in the formation of two Tesla coils to power up for the Final Charge. George tackles the Big Fish Boss and defeats him, but the threat is not yet over. Happyman and Green Monster must guide Young Mouthbottom and his nets to the Starship before Mouthbottom plans to visit Ratboy Genius and the Starship Genius crew must abandon their soon-to-be-electrically-charged starship.

All the Starship Genius crew members evacuate except for Clyde, who must stay and keep the ship on course for the Thunderbolt. George spends a few too many seconds pummeling the Big Fish Boss, and as a result, flies to the ship just as the Final Charge occurs.

The Galactic Superheroes crash-land on the Red Planet from the momentum of the Thunderbolt, where they remain stranded until the Red Planet story arc. George loses his memory from the crash, and wakes up to see his arms missing. The remaining crew members are picked up by Captain Bob, and Clyde emerges from the Starship at the beginning of the Minecraft Universe's timeline, where he parties with a familiar-looking caterpillar. The series concludes as Old Fingerhead and Young Mouthbottom finally manage to catch the Big Fish Boss, who holds two pairs of arms in his bruised jaws.