T3H Metroid Galaxy 2 is a twelve page "sequel" to T3H Metroid Galaxy. Although it is only one issue, and not a complete comic, it is still considered a sequel. The plot is a direct parody of Pirates of the Caribbean: Dead Man's Chest, although the comic was released a month before the movie came out and used leaked plot elemnts in the story.
"A short time ago, in a galaxy very close to us", the Flying Dutchman II, which is apparently a spaceship which vaguely resembles an Imperial Star Destroyer, is flying through space. Davy Jones says that Samus owes him her soul. In the Latham city jail, Samus, Oveur, and the Writer have only served 23 days of their one year sentence.
One of Davy Jones's minions arrives and breaks the jail cell down, intending to then capture Samus, however, the three heroes escape. They find Samus's ship and fly away, bombing the jail in the process. The see Ridley attacking some guards, and suddenly he appears on the ship with Mother Brain. Instead of explaining how they got in, Mother Brain tells Samus that she must find the "Dead Man's Chest", a chest that contains the key to defeating Davy Jones. King Dracog and Pickett appear on the ship as well and agree to help (it is unknow why they wish to help Samus, as in the series finale they testified against her).
Meanwhile, Davy Jones hires Sarge and his men to come help track down Samus. The Dead Man's Chest is tracked to the Caribbean. Sarge and Simmons go through their portal to the Caribbean, and Church and Caboose, wanting to know what they're up to, follow.
Mother Brain, Ridley, Dracog, and Pickett are surrounded by Davy Jones's minions on the beach, and Pickett gets headstrong and throws his bowler/derby hat at one, cutting its head off in a fashion similar to Oddjob's hat. The minions kill Pickett, giving the other three a chance to run away (Mother Brain breaks out of her tube during the escape). Sarge, Simmons, Church, and Caboose capture the three heroes and throw them in a cell for holding. Back in Blood Gulch, Donut and Grif throw a party due to Sarge and Simmons not being there, Tucker does the same at the Blue Base.
Back at their Caribbean holding cell, Oveur befriends Caboose and convinces him to set him free, leaving Samus and the Writer in the cell. Oveur knocks out Sarge and steals his armor, allowing him to pass by Simmons and Church without an issue.
After switching back to his regular armor, he frees Samus and the Writer. The four Blood Gulch characters are sucked back to their dimension. Samus and Oveur kill several of Davy Jones's minions. Meanwhile, the Writer encounters the monster from Lost in a "stupid Lost crossover". Samus and Oveur find the Dead Man's Chest.
They find the Writer and Samus shows him the Chest's contents: the heart of Davy Jones (which should "not be used around kittens, pregnant men, or Democrats").When they reach the beach, the S.S. Metroid, a sailboat, arrives, with the three villains on it. Dracog is angry about having to clean up the "Kraid droppings". Ridley fixes Mother Brain's tank. Suddenly, the Flying Dutchman II, which can travel on water, appears. The three villains abandon ship, floating on Mother Brain's tank.
When the Flying Dutchman II opens fire, it turns out the S.S. Metroid has cannons as well. The Writer tries to get from the S.S. Metroid to the Flying Dutchman II, but suddenly the Kraken appears from the waves.
The Writer confronts Davy Jones and they duel, with the Writer using his pencil as a sword. Davy Jones impales the Writer and leavs him to die. The Kraken grabs Oveur and is about to eat him when Sheila, piloted by Caboose, arrives and shoots it to death.
Sheila fires on Davy Jones as well. Samus tries to see if the Writer is okay while Oveur reuintes with Caboose.
Davy Jones throws his sword into Sheila's tank nozzle, forcing Caboose to return to Blood Gulch. Samus shoots the heart in Davy Jones's presence, killing him.
The three heroes run through the comic's various sets, cheering (they run through the Caribbean set, the Phazon set, the Dark Aether set, the Future City set, and then through a set that isn't done yet). Their parade is ended by the Latham police, who arrest the trio again and throw them back in jail. The issue ends with Samus thinking she forgot something.
After the credits, what Samus forgot is shown-Ridley, Dracog, and Mother Brain are left out at sea. Suddenly, a mysterious person arrives and asks for their help-the Future Writer. This is followed by a panel saying "T3H Metroid Galaxy 3: Coming Summer 2006"
In the deleted scene, Oveur tells Simmons that his name sounds Dutch-Irish. This continues a Red vs. Blue running gag in which various characters imply that Simmons is "of Latino persuasion" (which his voice actor actually is), while Simmons maintains that he's Dutch-Irish. Simmons is about to free Oveur for his nice comment when Sarge tells Simmons that, as someone who kisses up to Sarge frequently, he should know when someone is doing it to him, and Simmons tells Oveur not to try another escape method again.
- The plot is based off leaked plot elements from Pirates of the Caribbean: Dead Man's Chest.