Anyway. This arc's mission is the recovery of Michael Nowlan, who is a mutant with the power of enhancing other mutant powers. He's been taking drugs to suppress this, and has run away from the "Alliance of Evil", which consists of Tower (can manipulate his mass/size), Frenzy (invulnerability, strength) and two new characters: Stinger (who can discharge electricity) and Timeshadow (who has short range time travel). This Alliance reports to Apocalypse, and there's four of them, so I wonder if they were candidates for Horsemen (by all accounts Apocalypse was a last-minute replacement so this was not intended by the writers, but it's nonetheless an interesting coincidence).
They fail, and Michael is spirited away. This results in some introspection. This wouldn't have happened in the old days. I mentioned briefly before that the revived Jean is not a telepath. There seem to be two chief reasons for this. Firstly, a mobile telepath is way overpowered compared to the rest of the team - it's the same reason they rarely let Xavier be all three of walking, on the team, and telepathic. Secondly (as Teebore has pointed out in the comments for #1), if she were able to read people's minds, this whole plot with Scott and Madelyne wouldn't work, as Jean would know about it and insist on Scott doing right by Maddy, right? It's telling that the original Scott/Jean plot petered out more or less at the same time she got those powers in the first place. Scott has made that call to Maddy, by the way, and had no answer. He reckons she's left him. Which is completely ridiculous of him. He has left her. Jean reckons that Scott's in love with someone else... Phoenix. Actually, I can't see a good reason why she hasn't guessed there isn't another woman involved here?
Anyway, Michael knows X-Factor's secret, but was kindly keeping it. Apocalypse arrives fairly well-developed, being centuries old and wanting mutants to kill mutants so that the strongest will remain. Our final battle sees Michael kill himself rather than allow the Alliance and Apocalypse continued access to his power.
We don't know very much about Apocalypse, but he makes an instant impression in a way that immediately marks him out as an Important Villain. This (thanks Louise!) is X-Factor's first slam-dunk.