Not sure where you left off, but since you didn't mention the Alchemax building blowing up and the world flooding, we'll start there...
Series editor Joey Cavalieri was fired, and writer Peter David and artist Ron Lim quit as a result, in (mostly) mid-plot (ish #44). Miguel had just revealed himself to mom Conchata and biological dad Tyler Stone that he's Spider-Man, the Venom 2099 symbiote escaped having taken a new host (Roman), and thanks to Cavaleri's replacement throwing in a snippet of un-PAD dialogue the readership now thinks that Gabriel O'Hara is the Goblin.
Enter the new creative team.
Next issue has NYC under sev. hundred feet of water, in a jarring tie-in to the other 2099 series' 'Atlantis Rising Again!' plotline, itself a plot device providing a storyline reason to cancel all the books and kick-off a new series titled 2099:World of Tomorrow. Miguel confronts the Goblin, who reveals he's Gabe (but never actually takes the mask off) in issue #45, then the Vulture (in sh #46) who blows up Alchemax Tower during an invasion of Attuma-led Atlanteans who take advantage of a Phalanx-created worldwide flood to invade the (formerly) surface world for desecrating Namor's final resting place. Conchata is killed, Tyler is killed, Gabe/Goblin and the Vulture fly off never to be seen again, and Miguel boards a shuttle destined for the Savage Land. The dialogue and art is excellent, but the plot - well, it ain't any less confusing when you read it first-hand, trust me.
In 2099:World of Tomorrow, the survivors of the great flood try to restore civilization. Miguel runs around not wanting to be in charge of anything, and is transformed into an angst-ridden wreck who gives up the mask forever at the end of the series. The series manages some cool moments, but it's obvious that the writers and artists don't have a good handle on how the characters differ from their 20th century counterparts.
Miguel is last seen in 2099:Manifest Destiny, back at the head of Alchemax, and married to Xina Kwan, reunited with Gabriel (who wasn't the Goblin after all) and Conchata (who sued Doc-In-The-Box for falsely declaring her dead). Although Miguel never dons the mask in his last outing, he does manage to live another thousand years, aquiring an interesting new power along the way. Suffice it to say that, in writer Len Kaminsky's story, Miguel and GR2099 alter-ego Zero Cochrane prove themselves to be possibly the two most influential people of the entire history of Marvel Earth.
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