When last we left our cosmic heroes, Gamora had just accepted the Xandarian Worldmind into her head, and Gamora, Ben Grimm, and Sue Richards had been captured by Super-Skrull, because Commander K'lrt has decided he needs some help to protect the Skrull garden planet of Aks'lo.
It turns out, the Skrull Empire is a bit unconvinced that the Annihilation Wave is as awesome and destructive as has been reported, and that outer planets of the Skrull Empire have been told to dig in and repulse the invaders rather than evacuate.
Ultimately K'lrt hopes to lure Reed Richards onto the scene, because for a primative human he has shown a remarkable ability to think of solutions that fail to occur to anyone else.
K'lrt also managed to save another prisoner on the Kyln, who turns out to be Howard the Duck. Initially Super-Skrull ignores Howard, but Howard slowly begins to attempt to subvert Super-Skrull's companion, R'kin, in part by using alcohol. Essentially, Howard doesn't like being coerced into doing anything.
Ben attempts to shut down the ship's automated weapons, agreeing with Howard that he doesn't like being coerced into saving anyone, and Sue attempts to explain to the Super-Skrull that they will be willing to help on their own terms.
Unfortunately, Super-Skrull doesn't like losing control, a fight ensues, and the ship's hyperspace bubble starts to degenerate, threatening to crash the ship.
Howard wins R'kin to his side, and Howard and Sue work together to cover Super-Skrull with coolant and force fields to restrain him so that he will be more "pliable" to listen to his captive's plans. Super-Skrull changes shape to taunt Howard, but fails to smash the small bird creature, which devastates him, and allows Sue to finally trap him, while Ben manages to keep the ship from crashing.
Sue and Howard are attempting to convince the local Skrull military to evacuate the worlds on the edge of the Skrull Empire while Ben flies by the artillery beetles sent forward from the Arthrosian host, attempting to bomb them with the Skrull gunship they are on.
K'lrt, still furious with Howard, decides that it's still better to save as many Skrulls as possible, and gives his security clearance to the military representatives to help convince them to listen to Sue and Howard. R'kin modifies Howard's armor to make him sound more like Darth Vader as he attempts to convince the Skrull military that he is actually Lord Commander Mallard, final survivor of Duckworld, which was ravaged by the Annihilation Wave despite their proud and powerful space fleet.
Howard attempts to convince the Skrulls by talking about the Biblical plagues and how the massive capital ship coming through hyperspace is like Moby Dick, and the Skrulls are greatly confused. Ben jumps out of the ship to take on the last of the beetles hand to hand, and Sue, Howard, R'kin, and K'lrt finally convince the Skrulls to sound the evacuation order and to issue an evacuation order for all of the outlying worlds.
The planet is successfully evacuated, but as the team is retrieving Ben, the Harvester of Sorrows, a massive super weapon that converts matter in this universe to Negative Zone compatible energy sources arrives in the system and captures the Skrull gunship and our heroes, and Admiral Salo and his host attempt to take them prisoner so as to experiment on them to better know their enemies.