Following the events of the previous issue, Herman Smirch is wanted by the FBI as the main suspect in the hijacking of a 747 airliner. After pretending to the police that she has not seen him in months, Herman's mother comes to her son (who was hiding in her closet) and tells him the police is gone. She also gives him a package: his neighbour forwarded back the Game Boy he had given to his children, with a note saying she taught her kids not to accept gifts from strangers and especially not "weirdos" like Herman.
Convinced that he cannot get his mother involved in his situation with the Game Boy invaders, Herman decides to "borrow" some of her house money and her car. A week later, Herman is at Jerky's Burger Bar, contemplating that he should skip payment on his dinner as he finds the price outrageous. While the waitress is away serving another customer, he gets hypnotized into opening the gateway and summons Pionpi.
Going outside, Pionpi explains he came with a elite squadron to set up a base for Tatanga and enslave many giants. He asks Herman what is the world's largest population center, to which Herman answers China. Satisfied with the answer, Pionpi orders Herman to drive him to China and has his car modified to be able to fly. After a few hours of flight, Herman, who doesn't know where China is, lands into a unhabited island in the Pacific and tells Pionpi they're at the destination, pretending the lack of inhabitants is because it's monsoon season.
On the USS Nimitz, Ensign Greg Campbell points out to Jose there is a black cloud hanging over the island, but Jose merely tells him to go back to work. Later, inside his quarters, the mention of the black cloud leads to Greg rereading a letter from his brother Josh. The letter explains that the black cloud is a sign of Tatanga's presence and how to summon Mario by using the "middle door" in either of the first two levels of each world of Super Mario Land, but Gregg dismiss the letter as a product of his brother's hyperactive imagination.
In the afternoon, a off-duty Greg plays Super Mario Land and is shocked to find the goal has three doors instead of two. Mario goes through the middle door and enters reality, asking Greg where Tatanga is.
On the island, Tatanga's force are nearly finished fortifying their base.
Back on the deck of the Nimitz, Mario thanks Greg for his assistance in getting the Sky Pop out of the Game Boy and takes off to recon the island. Sensing something is wrong as he approaches the base, Mario is ambushed by Tatanga's forces, who are shooting with real ammunition. The Sky Pop is heavily damaged and Mario makes a crash landing on the deck of the Nimitz, Greg catching the plane as if it were a football.
Pionpi and the troopers rejoices at Mario's apparent defeat and their impending victory. Herman joins in their battle chant but Pionpi silences him, telling him the chant is only for Tatanga's loyal minions. A Gao rebuffs Pionpi, saying Herman is as much of a servant to Tatanga as them.
On the Nimitz, Mario reassures Greg he is fine and explains he is outmatched against Tatanga's real world weapons, requesting access to the ship's ordinances. Greg is initially hesitant but changes his mind, reasoning that, as the island is United States territory, it is his responsibility as a Ordnance Officer to bring the fight to Tatanga.
The next morning, two officers in the carrier's Air Operations Center, having found a piece of paper on the hangar deck, are beffudled by the blueprints for the Mario Sky Pop Defense System. Now heavily armed with Vulcan cannons, various type of missiles and laser-guided bombs, the Sky Pop flies by the carrier's control tower.
Mario flies to the island fortress again, but this time his new weapon systems make short work of the island defenders. As they detect one of the carrier's F/A-18 Hornet approaching the island, Pionpi orders the guns to fire on it, giving Mario the opening he needed to land. Mario throws a bomb from the Sky Pop's defense system to defeat a group of Gaos. A tank nearly sneaks up on Mario, but it destroyed by a blast from the F/A-18. Mario jumps into the command center and grabs Pionpi, but the main screen of the command console shows the F/A-18 has been heavily damaged and is about to crash. Mario flies to the F/A-18 and hold its wing, ensuring a safe landing.
Pionpi, recognizing the base is lost, activates its self-destruct countdown and orders Herman to escape. On the carrier's deck, Mario notices Tatanga's troops are escaping and jumps back into the Game Boy. A formation of US Navy's planes observes the destruction of the base and fly back to the carrier.
Herman Smirch flies back to the US Pacific coast and parks at a gas station to use the bathroom, content in the idea he's now one of Tatanga's top minions. While inside, his car flies up and dissapear. Heading back outside, Herman laments he forgot to put it on park.