@bigbadwolfx0: By Prof. X' and Magneto's monster I assume you mean Onslaught. Nate didn't actually fight Onslaught, he along with Franklin Richards was captured so Onslaught could absorb their powers..
As for Nate and Madelyn, no they were never a couple. Madelyn knew full well of their relation and used Nate's naivety to manipulate him. Nate had no idea of Madelyn's connection to Jean. And it never went any further then a kiss. His main relationship was always with Threnody, who may or may not have given birth to Nate's child.
Before I explain the shaman storyline it needs to been known that ever since his creation in the Age of Apocalypse Nate's powers have been slowly tearing his body apart.
The whole shaman thing came about after an alternate version of Madelyn, called Queen Jean, showed up and pretended to be the Madelyn that Nate had previously known. She takes Nate to her world where he finds out that this Madelyn has been searching the multiverse and collecting Nate Grey(s), as he/they are the most powerful psionic weapon in all existence. With Age of Apocalypse Nate Grey being the most powerful over all. Nate escapes and runs into another version of himself who had a special X tattoo, the genetic brand, which prevented his powers overloading. This alternate Nate calls himself a shaman, protecting people from Queen Jean's power.
The two Nate(s) end up getting recaptured by Queen Jean, but in order for the original Nate to escape the two Nate(s) switch bodies. So now AoA Nate has all his powers and the X tattoo to stop them killing him. The alternate Nate and Queen Jean end up dying and the original Nate ends up back on Earth-616 and vows to honer his alternate self by taking his role as shaman and to protect mutants and humans alike.
So no mater which reality she comes from Madelyn Pryer's relationship with Nate always feels a bit rapey on her part.
Nate spends the next few story lines doing the shaman thing protecting mutant/human kind and saving the multiverse. Until he ends up facing the Harvester, an alien with the ability to drain entire planets of their life-force. While it is outright stated that Nate is much more powerful than the Harvester, Nate can not hurt the Harvester without hurting all the people the Harvester has already connected too. Nate ends up converting himself and the Harvester into energy and merging with Earth's life-force, thereby tainting it and preventing others of the Harvester's species from 'eating' Earth.
Years later Nate would eventually separate himself from the Earth's life-force and returns to the physical realm in the Dark X-Men mini-series. A feat which Nate explained was incredibly difficult since he had become a part of every living thing on the planet. Nate possesses Norman Osborn for awhile and battles the Dark X-Men which ends up releasing Osborn's Green Goblin persona. Nate ends up getting his powers drained by Weapon Omega and Mimic and gets strapped into the Omega Machine.
Months pass before Nate is eventually rescued by the New Mutants, in the medic centre on Utopia Nate is informed that his powers have been incredibly damaged but they would return slowly, really slowly. On Utopia Nate bonds with Cyclops and Hope Summers before before moving in with and joining the New Mutants. It's at this point we see Nate's powers start to return as well as him starting a romance with the team's leader Dani Moonstar.
Nate was last seen in Fearless Defenders #9 where it's confirmed that he is still in a relationship with Dani, as well as talking to Dani's ex-boyfriend Cannonball.
That's pretty much everything up to date. Where is Nate now? I don't know, but I want him back A.S.A.P.
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