The Fantastic Four have just discovered that the woman they thought was Alicia Masters has actually been a Skrull spy. Furious at this deception, the Human Torch lashes out, demanding to the Skrull impostor tell him what happened to his wife. Reed tries to pull Johnny back before he can harm their captive, but he burns his hands because Johnny refuses to flame off. When the Torch takes another charge at the Skrull spy, Sue envelopes him in an invisible force field. When he uses his Nova Flame to try and free himself, he only succeeds in burning out all his oxygen, snuffing out of flame and knocking him out. Quickly coming around, Johnny is checked on by his teammates to make sure he is okay. Johnny is fine and has likewise regained some composure over the current situation and apologizes for lashing out earlier. With Johnny's outburst out of the way, Reed demands that the Skrull woman explain herself.
The Skrull introduces herself as Lyja, telling her that her presence among them was the result of years of planning on the behalf of the Skrull high command. She recounts back to when her commanding officer Commander Kalamari called a meeting among his command to discuss a means of destroying the Fantastic Four. When it was suggested that they create another Super-Skrull, Kalamari rejects the idea as the process is too cost prohibitive. Then a suggestion is made by Paibok, who suggests they use their natural shape-shifting abilities and subterfuge to replace someone close to the Fantastic Four in order to spy on the group. When Kalamari likes this idea, Paibok then suggests that they select a female Skrull to take the place of the Thing's then-girlfriend, Alicia Masters. Paibok then gathered a group of suitable candidates and eventually selected Lyja, either due to or in spite of a past relationship between the two. Lyja was then placed on a rigorous training session to learn everything she could about Alicia Masters in order to flawlessly replace her without anyone noticing. To complete the charade, Lyja was also fitted with special contact lenses that rendered her blind and trained how to get by with her other senses. When she was ready she was brought into Earth's orbit to wait for the right moment to strike.
That moment came when Johnny, Ben and Reed were kidnapped by the Beyonder to take part in the Secret Wars. The Skrulls then attacked Alicia at her home and gassed her, allowing Lyja to take her place. However when the Fantastic Four returned from Battleworld, it was without the Thing who decided to stay behind and selected the She-Hulk as his successor. In order to maintain a close connection with the Fantastic Four, Lyja then began seducing Johnny and forging a relationship with him. However, her infiltration was almost too good, as Lyja soon found herself legitimately falling in love with Johnny in spite of herself. Even with the explosive return of the Thing, which led to a brief argument over "Alicia" and Johnny's relationship, Lyja continued the charade for months. Eventually she and Johnny were married.
Having heard enough, Johnny calls Lyja a liar, not willing to believe that this Skrull is his wife. Lyja insists that it's all true and that she is pregnant with Johnny's child. This comes as a shock to Johnny and later he spends some time alone on the roof of the Four Freedoms Plaza to mourn over the situation. He is soon joined by Ben to provide his support, telling Johnny that they're all there for him. Meanwhile, down below, Reed is preparing a new space craft to mount a rescue mission to recover the real Alicia Masters from the Skrulls. Sue comes to check on her husband and he confides in her his frustration at being so easily fooled and how he should have been prepared. This all gets him thinking about the initial space flight that led to the birth of the Fantastic Four. Recounting how a combination of cosmic rays and abnormal sunspot activity would cause their ship to crash, or for the group to mutate the way they did. Although it did lead to the birth of the Fantastic Four, Reed tells his wife that since then he has been steadfast in not allowing carelessness to affect their lives. Changing the subject back to Lyja, Sue asks her husband if he thinks she is really pregnant with Johnny's child? Reed tells her he isn't sure that humans and Skrulls can actually produce offspring together, but tells he that perhaps they can look into it further after they rescue Alicia.
Meanwhile, in Central Park, the Thing meets with the Puppet Master to thank him for tipping them off to the fact that the Alicia who has been living among them has been an impostor. Before departing, he tells Phillip that they are going into space to rescue Alicia. Returning to his home, the Puppet Master reverts to type, blaming the Fantastic Four for his step-daughter's kidnapping and is happy that their mission to rescue her will also lead to the Fantastic Four's demise. However, the Puppet Master is suspicious of the Mad Thinker's goals and seeks to make sure that the Fantastic Four's destruction happens only after Alicia is returned to Earth safe and sound. Taking a puppet of King Cobra, the Puppet Master takes control of the villain, who is also a prisoner at the Vault in an cell across from the Mad Thinker. By the Puppet Master's command, the Cobra goes over to the bars of his cell and asks the Thinker what he is so smug about? The Thinker replies by telling him that he managed a "practical joke" on an old friend in his quest to destroy the Fantastic Four and he fell for it. The Thinker of course is aware that the Puppet Master is controlling his fellow inmate and thinks about how rich his victory is, recalling how he previously broke into the factory that constructed the shielding for the space ship that Reed has constructed and altered the plans so that the shields will fall apart while his foes are in deep space.
Back at the Four Freedoms Plaza, the Fantastic Four are about to leave when suddenly it's explained to Johnny that Lyja will be accompanying them. Hearing this, and seeing Lyja in one of Sue's old Fantastic Four uniforms angers Johnny who takes offence at the Skrull woman accompanying them. Reed orders Johnny to calm down, telling him that Lyja is their only means of knowing what they are up against in space and that they are making her wear the uniform so that they can differentiate her from other Skrulls. Lyja tries to appeal to Johnny, reminding him that he knows her better than anyone and knows that he can trust her. Johnny responds by telling her that he has never met her in his life and angrily boards the spaceship. After a quick call to JFK airport to get flight clearance, the Fantastic Four head off into space, their destination: the Andromeda Galaxy.
Lightyears away on the Skrull warworld, a massive military planetoid disguised as a barren world, Skrull technicians are busy experimenting on Paibok in order to turn him into another Super-Skrull. It is noted that the sessions are becoming less painful for him, but Paibok says the pain is worth being prepared for any contingency. The Fantastic Four soon arrive outside of warworld and with the help of Lyja's knowledge of the facility, they are able to land their ship within the hidden dreadnought without setting off alarms. However as soon as they exit the ship the Skrulls instantly recognize the intruders and the alarm is raised. The Fantastic Four fight back with the help of Lyja. Soon word reaches Paibok in security and he is more than pleased that the Fantastic Four are here. He soon greets them by showing off one of his new abilities: the power to project ice. Using his electrical powers, Paibok forces Reed to flee into a nearby vent in order to continue searching for Alicia. Paibok then turns himself into organic steel and begins battling it out with the Thing. When Ben knocks Paiboik down, he changes tactics and freezes Ben on the spot.
Meanwhile, Reed gets the drop of some Skrulls in a monitor room and begins accessing the Warworld mainframe to find out the location of Alicia. As the battle rages on, Paibok continues to gain the upper hand over the Thing, but Sue steps in with an invisible force field. But she is felled when Paibok blasts her with energy that can pass through the invisible force field and harm her. As Johnny battles other Skrulls, Paibok sneaks up behind him. Before Paibok can blast him from behind, Lyja calls out to him and dives in between them, taking the shot meant for Johnny. With Paibok gloating over killing this betrayer, he is distracted sufficiently enough for Ben to collapse and entire wall on the Skrull, burying him alive. Holding what appears to be the mortally wounded Lyja in his arms, Johnny tells her that he realizes that he does love her after all and believes her entire story. She then tells Johnny that there was no baby and she said as much to try and force him to stay with her. She then apologizes for all the hurt she has caused and with a final "I love you" seemingly dies in Johnny's arms.
Suddenly the self-destruct systems are activated, sounding an alarm that causes all the Skrulls to flee. This was set by Reed who has also located Alicia Masters location in the facility. Sue, Ben and Johnny flee back to their ship, leaving Lyja behind. As the Skrull crew begins to flee, Paibok calls them cowards and begins lashing out at them with his new powers. Meanwhile, Reed finds the stasis chamber where Alicia is being kept and rushes her back to the ship. As Paibok curses the Fantastic Four, the group escapes with their mission accomplished, making it safely away from War World just as the planetoid explodes. The Fantastic Four narrowly avoid getting out of the blast radius. As they head back to Earth as Alicia awakens. Johnny is the first one to her side, but when she becomes fully aware of her surroundings it is Ben she calls out to and hugs creating an awkward situation for everyone except for Alicia who has no idea how much time has passed or what has been going on in her absence.
At that very moment, just as the Mad Thinker had timed it, the shielding on their ship suddenly breaks loose. While Reed assesses the damage and reports back that the lack of shielding is not a major issue, however one of the broken pieces pierced their hyperdrive damaging it beyond repair, leaving them stranded in space.
