During an attack on the Earth by Galactus, he was defeated when Dr. Strange confronted him with the ghosts of all the beings slain on the worlds he devoured. He would have died had Reed Richards not intervened and spared his life. Galactus would then go on to destroy the Skrull Throneworld, leading to Reed's abduction into deep space and placement before a council made up of survivors of the worlds Galactus destroyed to stand trial. Reed's life was spared when Galactus made an appearance out of gratitude and brought along the cosmic entity known as Eternity to explain Galactus' role in existence. But, in this reality, Galactus does no such thing...
Without Galactus' appeal to sway the verdict of the council, Reed Richards was sentenced to death and executed immediately by Empress Lilandra of the Shi'ar Empire. The rest of the Fantastic Four, brought to observe the proceedings by Uatu the Watcher, were set to get revenge for their slain comrade when Uatu quickly transports them back to Earth. A few million light-years distance was not enough to quell their bloodlust, and the FF commandeered a Skrull saucer they had impounded on a previous adventure as well as Annihilus' Cosmic Control Rod. They took off for the Shi'ar Throneworld for their vengeance.
Meanwhile, Gladiator of the Shi'ar imperial guard was questioning Lilandra's decision, earning him an indefinite leave of absence from the planet. As his shuttle took off, Lilandra was alerted to the FF's ship entering their space. A ship flies out to meet them, but is quickly dispatched by the Human Torch while the Invisible Woman protected their own ship with her force fields.
Suddenly, the odds did not look in their favor as a good number of the Imperial Guard entered the fray. Sue took the Control Rod and placed it within the saucer's weapon systems. The combination created a blast so powerful it completely obliterated the Shi'ar planet. The FF return home, more depressed than when they left. Now not only have they lost a friend, but had unintentionally committed mass genocide.
Gladiator, the only survivor of the planet as well as the only witness to its destruction, called the delegate council to order once again to decide on the best retaliation for this transgression. Past tensions aside, now members of various alien races feared that they could have easily been the target...or next! This fear led to the unanimous decision to destroy Earth. However, another scheme is afoot. A Skrull had posed as a Kree in order to steal a device known as the Omni-Wave Projector. When used properly, it would project a virus between all the ships of the assembled attack fleet and destroy them all, with the blame falling on Earth; which coincidentally the Skrulls would claim as their new Throneworld in the aftermath.
On Earth, the FF hold a press conference to confess their sins to the world while alerting them to the possible event of a retaliation on the whole planet. The United Nations convenes and decides to place the command of all the world's armed forces with SHIELD, or more specifically Colonel Nick Fury, with additional help from the Avengers and other heroes in order to combat the alien threat.
The FF get some sage advice from little Franklin, Reed and Sue's son, who ponders why they don't try an apology. Deciding to try and talk to the alien armada before they reach Earth, the FF steal the UN confiscated Skrull saucer and take off back for space. On the way, however, they detected another Skrull ship in the area. Originally thinking it to be a glitch, they were set to bypass it until they found the actual ship and discovered its possession of the Omni-Wave. Remembering the tales from the Avengers about it from the Kree/Skrull war, the FF decide they're up to no good and prepare to stop them.
The armada drew ever closer and time was quickly running out. In a last-ditch effort, the FF attacked the Omni-Wave itself and destroyed it as well as the ship. The armada confronted the Earth but put their fears at ease when they conveyed they had received transmissions from the FF about the Skrulls' treachery and how they died to save the entire fleet. Gladiator offered Earth a chance to join in a new collective of the intelligent races across the cosmos to begin a new era of friendship and brotherhood. He awaits their answer.