But the doctor tells the Joes that the germ is not dying but is going through the stage of mitoesis, a process of cell division. And as Flint watches the two germs head in opposite directions, Scarlett notices that one of the germs is headed toward New York City.

Under a tree, Airtight tells the Joes that it looks like he failed, and Ace, who has a bandage around his tree, tells him, “Join the club.” Shipwreck explains that he believes that they could still poison the germ, however, Ace reminds Shipwreck that the insecticide didn’t work.
Shipwreck: “What we need is a candy-coating.”
Ace: “What you need is a transfer.”
But Airtight chimes in that Shipwreck might have a feasable idea. The doctor explains that apple seeds contain a very small amount of poison and adds that if the Joes can give the two germs enough poison, they might be able to stop the them.

Flying above the germ, Ace, Dusty and the other Joes take advantage of the germ’s mindlessness by firing missiles at the ground and causing the germ to move toward an apple orchard, but not enough apples are consumed. Therefore, the Joes destroy a cliff near another orchard and cause the germ to slide down and consume its final dose. The germ explodes and the residue splatters the Skystrikers.

Flint congratulates the Joes via a radio while he and Cover Girl watch several generic Joes load crates of apples onto Aramdillos, Sluggers, AWE Strikers and trucks. While traveling to the point of interception, the convoy is forced to halt due to a river that doesn’t have a bridge. Shipwreck learns from the driver that there is a blockade in the road so he kills time by making a pass at Cover Girl, who folds her arms, turns away from Shiprwreck and mutters, “Oh, brother.” Shipwreck then sits down next to her and soon receives a jab in the ribs for annoying her.

Flint radios for Tollbooth and his Bridgelayer, and after Tollbooth extends the bridge and drives over it, the Maulers and other Joe vehicles follow him. Flint tells Ace that they need his team to buy the Joes some time since they were delayed, so Ace fires his last missile at a dam and tries to drown the germ. But Bacteria X surfaces and continues to move toward New York City.

In front of a Slugger, Gung Ho stands beside Flint and the two wait for the germ to make its appearance, however, Shipwreck is impatient. So he jumps onto the roof a truck, raises his fists into the air and tells the germ that this battle will be its Waterloo, its Alamo. Suddenly the germ towers over Shipwreck and as Cover Girl shouts the sailor’s code-name, Shipwreck tells the germ in a frightened voice, “Ju- just kiddin’, big guy.”

Grunt pours apples into Roadblock’s bazooka and then fires it while Thunder, Rock ‘n’ Roll, Quick Kick and Snake Eyes ride on AWE Strikers and shoot at the germ, but it continues to advance. Unsure how to stop the germ, Cover Girl tells Shipwreck that he should ask it out on a date. Flint orders the Joes to dive into the river, however, Shipwreck remains behind and continues to toss one apple after another and shouting, “This might be the one!”

Cover Girl tells Shipwreck that if he leaves with her now then she will go out on a date with him. They fall off the roof and Shipwreck happily exclaims, “Anchors away!” Shipwreck is told that they will go on a date as soon as possible and that they will go swimming. And as the two dive into the river with the other Joes, Shipwreck shouts, “This is the best date I’ve had in weeks!"

Ace and his Skystriker team arrive and dump more apples from the cargo bays in the planes into the germ, which effectively ends the germ’s life. Spirit and the other Joes watch the germ explode and the same disgusting residue that splattered the Skystrikers earlier covers the Joes.

The two Cobra Eels who were trapped inside the germ fall into the river with the Joes and Roadblock comments, "It must be a worm from the germ."

"I guess that germ found Cobra as hard to swallow as we do," adds Gung Ho, and the Cobra Eel in Roadblock’s grasp looks around and listens to the Joes laughing at him.