The story of how she got brought back in Fantastic Four is pretty interesting. Mark Gruenwald wanted to do an "X-Men West Coast" book with the O5, but Louise Simonson, the editor of Uncanny X-Men and someone aligned with Claremont's vision, blocked it. Bob Layton I believe pitched an O5 reunion because X-Men was so hot as a property. Jim Shooter liked the idea of another X-Men book, but there was a dispute over the status of Jean. Claremont was adamantly against bringing her back, and Dazzler was seen as an option. In her own series, she leaves with Beast with the idea that she would be the 5th member of X-Factor. But Jim Shooter was still open to the idea of Jean Grey returning despite being the one who insisted she died.

Shooter was willing to bring her back, but only if she was absolutely, and completely absolved of anything that happened while she was Phoenix.

Kurt Busiek, who was not yet the famous writer he is today, made a game of it. He famously hated that Jean died and has always been fond of Silver Age X-Men, and so, operating under Jim Shooter's rules, he told Mark Gruenwald about a way to bring her back that would also absolve her. That's the cocoon retcon. It was Busiek's idea (but I have to stress, Busiek is an excellent writer and this very contrived retcon was something he came up with for fun, while operating under the strict Jim Shooter guidelines of totally absolving her) and it found its way from the person Busiek told it too (Gruenwald I think?) all the way up to Shooter himself. And Shooter agreed to do it.

Claremont wanted nothing to do with it because he was so upset about it (he even proposed Sara Grey being the X-Factor member instead) and so they couldn't do it in Uncanny X-Men. But John Byrne always felt a little bad that Jean had died (possibly because it was his artistic license that got her killed) and he was happy to have a chance to rectify it. So in Byrne's Fantastic Four is where Jean is fished out of the bottom of Jamaica Bay.

Of course, Byrne committed fully to the idea of Jean and Phoenix being entirely, totally separate entities and wrote it that way. But that must have bothered Claremont, because Jim Shooter ended up rewriting some of the pages of Fantastic Four to more closely reflect that Phoenix had Jean's soul and was her in a way. Byrne was now upset that they changed his work after he was so happy to help, and had his name taken off the credits of the issue. Jackson Guice (RIP) was brought in to make the last minute art changes.

And so that's how Jean was brought back. Was it a good creative decision? Most would say no, arguing that it cheapened Jean's death in Dark Phoenix Saga. But I would argue Claremont had already cheapened her death by introducing Rachel and Phoenix again. Commercially, X-Factor was a huge hit, and its success is what helped lead to the ever expanding X-Men line that culminated in a giant boom in the early '90s, followed by a crash in the later end of that decade. I think if you asked Jim Shooter if he'd do it all over again, he would argue yes. The man was hard headed in his editorial decisions, but he loved a buck more than any of that.