In a Nutshell
Cyclops is forced to send his son into the future to save his life.
Plot: Jim Lee & Whilce Portacio
Script: Chris Claremont
Penciler: Whilce Portacio
Inker: Art Thibert
Letterer: Michael Heisler
Colorist: Dana Moreshead
Editor: Bob Harras
Editor-in-Chief: Tom DeFalco
Face to face with the massive Apocalypse, X-Factor is attacked by the Riders of the Storm and brainwashed Inhumans Medusa and Crystal. Overpowered, they are captured, and Apocalypse gloats that he will use their power to increase his own. However, just then Black Bolt and the free Inhumans counterattack, just as Cyclops and Black Bolt had planned. However, Nathan has been infected with a virus by Apocalypse, and is dying. He instinctively pulls Jean into his mind to face an avatar of Apocalypse, and Jean proceeds to bring Cyclops in as well, who manages to defeat the avatar. Returning to the physical world, Cyclops blasts Apocalypse, destroying him, but Nathan is still dying, and Beast says there's no way to cure him in time. However, Askani declares that she can save him, by taking him with her back to the future, and Cyclops reluctantly says goodbye to his son in order to save his life. In the aftermath, the Watcher once more comments on humanity, applauding Cyclops for choosing hope over despair.
Firsts and Other Notables
Nathan Christopher, infected with a life-threatening virus by Apocalypse, is sent into the future with Askani this issue, thereby ending the relatively brief period of time in which Cyclops had an infant son.
Of course, we now know that Nathan will eventually grow up and return to this time as Cable, and this issue continues to hint at that idea pretty hard, both intentionally and in hindsight.
Most notably, the final page of the issue, which features the Watcher waxing philosophical on the nature of humanity a la the final page of "The Dark Phoenix Saga", has a cluster of weird crystal things on the bottom of the page, depicting four different images. The largest is of Nathan as a boy; the bottom two are, I believe, Professor X and Colossus, depicting happenings in the "Muir Island Saga" (they look to be drawn by Andy Kubert, who pencils X-Men #279, the chapter of that story in which Xavier battles the possessed Colossus). The final image, positioned just below Nathan, is of Cable, and seems to be there for no other reason than to link Nathan and Cable in the minds of readers. In hindsight, it almost reads like "don't be sad for Nathan, he's already back in the form of Cable!".
More indirectly, as he's dying, Nathan pulls Jean into his mind to help fight the virus (manifesting on the Astral Plane as Apocalypse), shades of the telepathic skills Cable will eventually be revealed to have, while Jean notes his raw power (with Cable later established as one of the most supremely powerful of mutants, albeit with his power held in check by the constant need to fight the virus).
The virus with which Nathan was infected is never referred to as techno-organic in this issue (it retroactively becomes that when it's established that Cable's bionics are the result of the T-O virus he was infected with here); instead, its described as basically being an advanced form of cancer, killing Nate cell-by-cell and inhibiting his body's ability to make more cells, though the art definitely depicts some kind of cybernetic effect, fitting the later retcon.
Ship remaining consciousness (represented as a little yellow ball of light) merges with Nathan this issue, in an attempt to help stave off the virus. He ends up going into the future with Nathan, where, it'll eventually be revealed, he lives on as Professor, the sentient computer system which runs Cable's orbital base of operations (which at this point had yet to be introduced). But for all intents and purposes, this marks the end of Ship.
Askani makes a point of saying that she won't be able to bring Nathan back from the future once he's cured, as she won't have enough energy to make a return trip, and she's the only one who can do it.
This is the last we'll see of Apocalypse for awhile, until he returns in "X-Cutioner's Song".
Remember the Twelve? The mutants prophesied to save/lead mutantkind, first mentioned by Master Mold back in issue #14? Well, they get another mention here, with Cable seemingly added to their ranks (we also see images of Professor X, Storm, and maybe Cannonball and Legion); Apocalypse now seems to be placing himself in opposition to the group (he claims killing Nathan will seal their fate, an idea teased last issue, and which kinda fits the later revelation that Cable is destined to defeat Apocalypse once and for all), though in issue #14. it was implied he was part of the group. I think this might be the last mention of the Twelve until the storyline finally gets resolved (poorly) in the late 90s.
Inhumans Medusa (Black Bolt's wife) and Crystal both appear briefly in this story, as brainwashed thralls of Apocalypse, though Crystal also appeared in issue #67 amongst the free Inhumans (I guess she got captured and brainwashed between issues). She will shortly join the Avengers (the issue which leads to her joining the team is on sale the same time as this issue).
The narrative captions in this issue are written in the first person, from Cyclops' perspective, thus allowing Claremont to add some depth to what is, essentially, an issue-long fight scene.
In a nice bit of metacommentary, Cyclops notes that while villains and some heroes seem to die and come back, only the innocent truly die. Indeed, in comics, the Uncle Bens and Sharon Kellys of the world stay dead, while nearly every hero or villain who dies eventually comes back.
This is, effectively, the final traditional issue of this iteration of X-Factor. Portacio is on hand for next issue, but that one is in service to the larger "Muir Island Saga" story and is more concerned with moving X-Factor back to the X-Men, now that their base and supporting cast is gone, with issue #70 serving as an epilogue to that story, written by incoming series writer Peter David, and barely featuring any of this iteration's team members.
A Work in Progress
Cyclops says that he's realized the purpose of X-Factor is to protect people like his son from people like Apocalypse.
Apocalypse declares that the reason he's always fought to separate the weak from the strong is so that he can absorb the energy of the strong to increase his own power and become a celestial menace. This could be an attempt by Claremont to move forward the idea that Apocalypse is somehow connected to the Celestials (since Ship is from them as well). Then again, since Simonson is well out the door at this point, it could also just be Claremont trying to add some more gravitas to Apocalypse. Either way, it never really goes anywhere.
Cyclops notes that unlike in previous battles, Apocalypse isn't shapeshifting in this one, another idea which doesn't really payoff (unless the implication is supposed to be that this means Apocalypse is weaker, and thus more vulnerable to Cyclop's ultimately-successful approach of "blast him really hard").
Askani explains her "kinsmen" comment to have a more general meaning, basically a "well, we're ALL children of the Earth, right?" kind of thing.
Askani refers to her family as "me and mine", while Apocalypse refers to himself as "a body".
Like a Phoenix, From the Ashes
In addition to the Watcher's appearance on the final page, Cyclops is brought into Nate's mind to help battle Apocalypse, and he references the time he fought a similar psychic duel for the life of Jean in "Dark Phoenix".
I really like this issue. I say that up front because, try as I might, it's hard for me to be objective about it. Being a huge Cyclops and Cable fan, I read this issue a ton as a kid, and it always felt meaningful to me, moreso than the other issues around it (and being published at the time I was reading it). Of course, reading it now, I realize that was intentional: tasked with clearing the deck in anticipation of the new direction of the series, this story accomplishes that goal. Ship is gone, Cyclops' son is gone, Jean's telepathy is back (sort of), and some measure of finality on the subject of X-Factor and Apocalypse is provided. But the creators involved (I tend to give the credit to Claremont, but Lee and Portacio, as plotters, deserve some too) manage to turn what could have been a very mercenary, by-the-numbers story ("oh, and get rid of the baby, too! Can't have our heroes being family men!") into something more than that.
The allusions to "Dark Phoenix Saga", begun last issue but doubled down in this issue, with Cyclops' sacrifice of Nathan Christopher compared to Jean's sacrifice in X-Men #137, as well as a final page soliloquy from the Watcher on the wonders of humanity are, objectively, a pretty cheap source of drama. Claremont has certainly been dinged in the past for mining one of his greatest hits in order to inject some gravitas into a lesser story, and he's shameless about doing it here. But I'll be damned if it still somehow doesn't work, and that by the time Cyclops is once again forced to stand by and watch someone that he loves be taken from him before his eyes, I don't get a little verklempt.
But in addition to all the angst involving Nathan, Claremont (and I'm more inclined to credit him solo here, as most of this comes through via narration and dialogue) also manages to turn this story into a sort of thesis statement on X-Factor's existence up to this point. On the very first page, he rightly hangs a lampshade on the notion of Apocalyps being X-Factor's Magneto: he was there (almost) from the beginning, nearly destroyed the team by transforming Warren into Archangel, and has now handed them their greatest loss in infecting Nathan and forcing Cyclops to give him up. There's a lot of other stories between his scattered appearances, but one could read X-Factor as the story of the conflict between X-Factor and Apocalypse, something this story, and particularly this issue, codifies (and, though no good villain stays dead, it's clear that Claremont intended this to be something of a final word on Apocalypse at the time).
Additionally, Claremont attempts to give Cyclops something of a character arc here (and complete the redemption of the character destroyed by the early issues of this series), suggesting that X-Factor has been about Cyclops coming to terms with his place and role within Xavier's dream, and accepting that a normal life isn't in the cards from him, going from the hideous man-child of the misguided Layton/Guice days, who left his wife and child to play with his friends, to the angsty Cyclops of Simonson, believing Xavier trained him to be nothing more than a soldier, to the more measured Cyclops of this story, who realizes that, ultimately, the goal of X-Factor and of Xavier is simply to help those who cannot help themselves, and that he's at peace with that being his life. If X-Factor is the story of the title characters' ongoing battle with Apocalypse, it may also be about Cyclops accepting his role, not as a student of Xavier's or a solider in his army, but as a hero.
Again, this issue is far from perfect: the plotting is wonky (Apocalypse is defeated when Cyclops just blasts him really, really, hard), the Inhumans continue to not really add anything to the proceedings, and the art is messy, unfocused, and occasionally at odds with the scripting, with characters just dropping in and out at random. But for the conclusion to a story whose main purpose was to make the characters more palatable for their upcoming back-to-basics roles, it's far better than it has any right to be. On paper, "Cyclops sends his son, infected with a cyber virus by an eternal shape-changing mutant, into the future with a strange woman" is patently ludicrous. But as he's done for much of his fifteen years writing about the X-Men, Claremont manages to drill down past the more out-there trappings of the genre to lay bare the heart of the story: a father saving his son's life, but at the cost of experiencing that life with him.
Next week: Excalibur: Possession, and a pair of Wolverine issues, as the series goes bi-weekly again, #41 and #42.