The Fantastic Four interrogate Lyja, and learn that she replaced Alicia while they were away at the Secret War. Her intent was to get at the team through Ben, but he didn't return, so she went through Johnny instead. She soon found herself in love with Johnny, and felt divided loyalties. She agrees to help the team rescue Alicia in exchange for her freedom, so she goes with them to free her. They enter the containment centre, and fight their way through several Skrulls, including Paibok. They escape with Alicia, but Lyja and Paibok are left behind. (Lyja took a blast intended to kill Johnny, and Paibok was buried under rubble.) During their escape, the Mad Thinker's sabotage of their vessel does not destroy them as intended, but it does render their hyperdrive useless.

This 30th Anniversary issue then goes on to a note from Stan Lee, including some of his original scripted pages, followed by pinups and descriptions of Blastaar, Annihilus, Molecule Man, Rama-Tut, Dr. Doom, Mr. Fantastic, Invisible Woman, the Thing, the Human Torch, and Four Freedoms Plaza. This, in turn, is followed by a retrospective by Peter Sanderson, and a series of "Milestone" events.

The issue wraps up with "A Tale of Doom: The Official Story," depicting some of Doom's revisionist history policies.