Well, the Clone Saga happened : many clones of Peter and one of Gwen Stacy appeared. The Gwen Stacy one was fused to the Carnage creature, which poses problem when she gets stressed out or scared. The only clones of Peter to survive are The Scorpion and Spider-Woman. Doc Ock was revealed as the one behind the experiments, while the CIA are the ones who hired him to perform them.
The Warriors arc : good Kingpin story, with guest-starring from Daredevil, Moon Knight, Iron Fist, Doctor Strange. Kitty Pryde of the X-Men kicked herself out of the team and ends up going to school with Peter and the gang.
The Death of a Globlin story : Norman escapes once again, and at the end of the story it looks like both Goblins, Green and Hob, Norman and Harry, are dead.
The Amazing Friends arc : Liz Allan turns out to be a mutant, Kong reveals that he knows about Peter's secret identity, Liz goes with the X-Men and it's revealed that her father is the Blob.
The Shocker one-shot : poor Herman finally manages to knock out and capture Spider-Man. Yet another villain knows his face, and we learn more about Roxxon Corp, and we wonder what they're up to.
The War of the Symbiotes story : many flashbacks make that one kind of hard to follow. We see Eddie Brock as the Venom parasite makes him kill and eat people. The Beetle appears, intent on finding samples of the suit for a mysterious master. The Gwen Stacy clone escapes S.H.I.E.L.D's custody during Norman's escape from Death of a Goblin, she goes to Peter for help, Eddie comes to Peter because he wants the Venom suit back (he lost it before in the story). When coming close to Eddie who still had some remnants of the suit in his system, Gwen transforms into Carnage, a battle ensues, in which Venom completely absorbs the Carnage suit, making a new version of Venom and completely cleansing Gwen of any 'suit'. The Gwen clone is so perfect on every level that Tony Stark says there is no difference between her and the original Gwen, so May and Peter decide to take her back with them. Gwen comes back to life, basically.
The Ultimatum tie-in : Spidey saves people, teams up with the Hulk and nearly dies. JJJ has an epiphany and decides to completely support Spidey from now on.
The reboot under Ultimate Comics Spider-Man : Bobby Drake and Johnny Storm end up living at Aunt May's house. Mysterio kills the Kingpin. Peter and Gwen are dating. Introduction of The Bombshells, a mother/daughter duo of robbers. Kitty is doing some vigilante work as the Shroud, and has developed her powers to become super-dense, giving her super-strength and a very hard to move body.
The Chameleons arc : starts off with Kitty being arrested during school for being a mutant, which leads her to snap and attack a news crew at her house, followed by a fight with her friends. Kong goes with her. After that, the Chameleon captures Peter and takes his place, making a mess of Peter's life. The Chameleon are actually a brother and a sister, both with the same powers. They also captured Jonah, who figures out Peter's secret identity and becomes even more set on defending Spider-Man.
The following issues deal with the aftermath of the Chameleon arc, Gwen leaving the house temporarily, Carol Danvers deciding that it's time to deal with Peter's situation and arranging for people from The Ultimates to 'train' him. Gwen returns and decides that it will be a better idea for her and Peter to break up.
Bendis made it quite clear that they had a sibling-like relationship - one that both characters reaffirmed several times.
t: . I can't believe that Tony made something so unimaginably stupid, although his cover-up was funny.
