Issue #1 was the “assemble the team and introduce one new character” issue—a pretty standard launching pad, so this issue should be establishing what the ongoing conflicts will be.
The first is Scott and Jean and Scott’s wife Madelyne. Scott is basically an emotional infant. He seems to have fallen in love with Madelyne just because she looked like Jean, and now that Jean has been resurrected from the Hudson River he finds he still loves Jean but now he has a babymomma (and a baby Cable as well!). Rather than talk this out, he shoots the telephone with his eye beams when he learns his wife, who has grown tired of his bullshit, changed her phone number without telling him.
The “villain” of this episode is a new mutant called Tower who is basically a mutant version of Giant-man.
He’s on a mission to kidnap Beast and take him to an evil scientist whose son, Artie, looks like a Close Encounters alien.
Artie has psychic powers as well. Professor Maddicks wants Beast to help him reverse his boy’s mutation.
X-Factor rescue Beast just as he’s being experimented on, the lab explodes, and Professor Maddicks dies during their escape. The big result of the experiment?
Beast still has blue hair, but only on the top of his head—he’s otherwise reverted to a fleshy body again, thus making X-Factor even more like the original X-Men.