It's interesting that fandom doesn't hold any single creator to account for what happened to Cyclops - not Chris Claremont, the man who created Madelyne; not Bob Layton, the one who broke them up; not Louise Simonson, who assisted Claremont in delving into Madelyne's true origins. It's most interesting that the one who shoulders the blame in the eyes of fandom is Cyclops himself, as though a fictional character had true control over his character development! It really speaks to how much fans have invested in the X-Men's members, but it's certainly worked against Cyclops for the last 30 years as he's never fully crawled out from under the cloud of X-Factor #1.
Let's begin with the first perpetrator: Chris Claremont. Having killed Jean Grey in 1980, Claremont embarked on an unusual subplot for Cyclops in 1983 as the still-grieving hero met Madelyne Pryor, a woman with a remarkable resemblance to Jean Grey (or so every character claimed - Paul Smith's Madelyne looked nothing like Dave Cockrum or John Byrne's Jean; I don't believe the two ever did look alike until Marc Silvestri took over). This being comic books, naturally readers were led on to assume that Madelyne was somehow Jean Grey brought back to life, or at least someone with a connection to Jean. However, in a subversive climax, the subplot ended with all the seeming connections revealed as remarkable coincidences; Cyclops and Madelyne were wed.
Comic book readers and writers hate coincidences.
Recall that earlier in the X-Men mythos, Lorna Dane had been suggested as Magneto's daughter simply because the two had the same powers; that plot ended with the familial connection revealed as bogus, yet 30 years later Lorna would be (off-panel) made Magneto's daughter officially. When characters have similar surnames, powers or (seriously) hairstyles, regardless of what the initial creators intended, someone will assert "there are no coincidences!" and cement the connection in print.
Thus, regardless of what point Claremont intended to make with the initial Madelyne story, comicdom's disbelief in coincidence - coupled with Jean's resurrection - worked against that tale. Also working against Claremont (and more to the point, Cyclops) is comicdom's inability to allow characters to reach endings, no matter how well the ending is performed. Cyclops seemed to be set for a life of marital bliss with Madelyne, but editorial demands to have him participate in the Secret Wars crossover caused him to be spirited away during his own honeymoon. This frightened Madelyne, but she did her best to be understanding.
A year and half later, Cyclops returned to the X-Men (with a pregnant Madelyne in tow) to be present for Xavier, who appeared to be on his deathbed. This led Cyclops to be called away on two back-to-back missions, first to save the New Mutants from Asgard, then to be present at Magneto's appearance before the International Court in Europe. Thus, Cyclops was struck by three significant moments of upheaval: dealing with Xavier's departure (as he left the galaxy with the Starjammers), Magneto's ascension to head of Xavier's school and missing the birth of his son, Nathan.
In the aftermath of the birth, Madelyne noted nearly all of the X-Men who went to Asgard had called her to let her know they were in Europe - but not her own husband. She told Storm: "I understand Scott's not being here... but he should have at least let me know he cared." Although at this time the X-Men had been led by Nightcrawler (in Storm's absence since she lost her powers), Cyclops now intended to resume leadership of the X-Men, a role he hadn't officially held since Jean's death 6 years earlier. Cyclops rationalized this to Madelyne as needing to keep an eye on Magneto, although internally he felt Xavier was his true father and he should be the one to carry on said father's work. However, Storm had now returned to the team and she disputed Cyclops' bid. Despite her power loss, Storm faced Cyclops in combat and defeated him, proving true friends will kick your butt for you when you need it. Storm resumed leadership and Cyclops could then remain safely retired. Another happy ending!
One month later... X-Factor #1. Up until this point, Madelyne has remained sympathetic, never nagging or behaving shrewishly to Scott. Even as Cyclops engaged in combat with Storm, she knew that no matter how the fight ended her husband would wind up being hurt - either by losing leadership or by losing her because she intended to return to Alaska regardless. All of that, however, came from her creator, Claremont. To Bob Layton, Madelyne Pryor was an obstacle to getting the original nostalgic five X-Men back together and he worked quickly to turn readers against Madelyne, no doubt hoping they would be less troubled by Cyclops' actions, since for Scott to join X-Factor he would have to essentially abandon his wife and son - hardly a heroic decision. The first blow against Madelyne fell while the couple were at home in Alaska and Scott was distracted by a television news report about the Mutant Registration Act. Furious, Madelyne cattily yelled: "Haven't you done enough for them already? Isn't it about time they did something for themselves?" Given that she married a mutant and might have (later confirmed positively) given birth to a mutant, one would think Madelyne might share her husband's interest in mutant affairs. Heck, if she had steered him into being a political activist maybe he wouldn't have become a globe-trotting adventurer again.
Still, Madelyne dug deeper.
"You have a responsibility to your family now! I can't be the only one working on this marriage! We're supposed to be in this together, aren't we? Don't you think I know the only reason you came back to us at all is that you bombed out in your bid to lead the X-Men? Don't you think it hurts knowing that? Just like it hurts knowing why you married me in the first place! Because I reminded you of your old flame -- the late, but not forgotten Jean Grey!"
"I love you, Scott, and the X-Men don't need you! Jean is dead! I'm the one that needs you!"
It's strange that the character assassination of Cyclops would begin by bringing down his wife, but there it is. In one month, Madelyne went from a troubled but loyal partner to an ultimatum-delivering shrew. To put it in terms of tropes you would find on TV police dramas, she went from being the police captain's wife to the duty-driven detective's ex-wife. Although Layton couldn't have known it, he was grooming readers to eventually accept Madelyne's transformation into a demonic super-villainess. Later that evening, Madelyne found Scott brooding on their balcony. She began to apologize, not wanting to "lose what we have." Scott retorted, "I'm... just not exactly sure what we do have anymore." When she pressed him, he admitted he'd been thinking about Jean Grey.
The very next day, Scott received a call from the Angel, informing him that Jean was back from the dead and in New York. It should be noted that the Angel was an inactive X-Man and that Madelyne didn't know Jean was alive (and wouldn't learn this for years' worth of stories). Regardless, this was how the conversation which ended their marriage played out (presented in its entirety):
"Darling? What is it? What did Warren want?"
"He... er... needs me to meet him in New York -- today!"
"Well -- tell him you can't make it!"
"I - I can't do that, Maddy!"
"Scott Summers! If you walk out that door -- don't bother coming back!"
"I'm -- sorry, Maddy! I have to go!"
Cyclops was reunited with Jean, but simply seeing her alive drove him to the brink of mental collapse, unable to reconcile his never-forgotten love for her with his devotion to Madelyne and his son. In fact, he wound up wandering around the pier where the Phoenix first appeared and when Beast and Iceman found him, he poured out his heart about Jean and Madelyne. Proving themselves inferior friends to Storm, the duo encouraged him: "We have a second chance -- all of us -- to do something beneficial! Like it was in the old days -- the five of us -- together!" He still wasn't completely convinced, but carried on for Jean's sake. "Look -- if not for anything else, do it because I want you to be with me, okay?" Jean asked. "That's the only reason I'm still here, Jean!" Scott answered.
And sure enough, with the blessings of nostalgia the X-Factor team came together and by going on their first adventure (saving Rusty Collins) Cyclops found his footing in adventure. This would remain a touchstone for some time, as Cyclops would range from non-verbal to shell-shocked while out of costume but confident and capable while in combat. Layton pushed that in the audience's faces as best as he could in the first issue with Cyclops saving the entire team at one point and thinking: "Jean -- all of my friends -- would be dead by now if I hadn't come with them! If I wasn't here... I would have lost her again! And the boy, Rusty, would have died without a chance for a decent life! Of the group, only I have the power to save us now! Finally, I realize what I need to do and -- we will be free!!" For a man who at the time must have still been under thirty years old, under Layton's pen Cyclops certainly read like a man suffering his mid-life crisis.
Despite his breakthrough in the climax of X-Factor #1, Cyclops remained a wet blanket through Layton's work. In the second issue, Angel took Cyclops to task for not contacting Madelyne or telling Jean about his wife. Scott finally dug up the courage to call Madelyne, only to find she had disconnected the phone, evidently literally meaning it when she told him "don't bother coming back." Madelyne & Nathan couuld have been part of X-Factor's ongoing supporting cast, but it would have pushed back against the nostalgic get-the-band-back-together voice of the series. And so Cyclops would angst for the rest of Layton's run, until succeeding author Louise Simonson finally pushed things forward by having Jean learn of Madelyne, sent Cyclops back to Alaska and finally had Cyclops suffer the mental collapse which Layton seemed to have foreshadowed (and seriously, X-Factor #18, where Cyclops went crazy? hands-down my favourite issue of the series).
At the same time, Claremont adopted Madelyne back into the pages of Uncanny X-Men, with Cyclops' abandonment of her proving a good justification to turn the X-Men team against X-Factor (especially Scott's brother, Havok) and all of that came to a boil in 1989's Inferno crossover. Of course, it was during Inferno that Madelyne became a true, full-on villain and was forever redefined as Jean Grey's clone (in retrospect, Cyclops should have looked up her friends from high school before marrying her). Madelyne died in Inferno, leaving Scott & Jean to care for baby Nathan (until editorial demanded he be written out of Scott's life for the second time).
Cyclops has been made to do plenty of disagreeable things outside of his marriage to Madelyne: he built a mutant isolationist empire, threatened to assassinate politicians, created a personal hit squad, murdered his father figure and tolerated Emma Frost's fake British accent. Yet for many fans, his original sin was leaving his wife and child to return to Jean Grey - never mind that he and Jean weren't a couple (not until Fall of the Mutants, two years into X-Factor's run), never mind that Madelyne had behaved like an ogre with her ultimatums and cutting off access. Heroes overcome obstacles. Heroes find solutions. Heroes do the right thing. If Cyclops couldn't stand up for his family, how could anyone expect him to stand up for a world of strangers?
(An aside: re-reading Uncanny X-Men #201 for this post, I was really struck by the scene where Rachel Summers first met baby Nathan and vowed to protect him. Reflecting on all that Rachel & Nathan have been through over the years, it is heartwarming to see their siblings-by-another-mother relationship, from Rachel racing into the events of Inferno to try and save him to the fully-grown Cable journeying to the end of time to rescue her! Perhaps I'm projecting my own relationship with my older sister upon them, but I really like Rachel & Nathan.)