Shortly before the "Onslaught" storyline, Nate began to be sporadically referred to as X-Man, without explanation for the in-universe origin of the code name.

When sales began to wane in 2000, the series was revamped by Warren Ellis as part of the Revolution event beginning with issue 64 with Nate under the name of Shaman.

During this time, he unintentionally contributes to the eventual manifestation of Onslaught: Nate senses Xavier's astral form spying on him, and drags him into the real world.

After rescuing her from the Marauders, the pair form a mutually beneficial partnership: Nate provides protection, while Threnody acts as his guide to the world.

Their relationship deepens despite Nate's lingering doubts on her connection to Sinister, but Threnody eventually leaves, unwilling to answer questions about her past.

Nate tries to separate Aurora from the Brotherhood, but quickly learns that due to her personality shifts, she needs treatment that Dark Beast can best provide.

Nate survives due to the timely return of his telekinetics at their peak, but collapses from exhaustion in New York, where he is found and cared for by three mysterious girls named Jam (Jasmine Archer), Marita, and Bux.

Soon after, Nate is telepathically alerted by Cable that he is the only one close enough to protect the children of Jean's sister, Sara Grey, from the Prime Sentinels of Operation: Zero Tolerance.

The plan backfires: Nate resists being controlled, and upon learning that Jam's healed arm was only a solid psionic projection, he loses faith in himself.

During this they meet and are constantly shadowed by Ness, a member of the secret human/demon hybrid race, the Hellbent, who also had a vision that Nate would soon be responsible for the destruction of the planet.

[23] Nate was also continually hunted by Operation: Gauntlet, a special task force of the United Nations, who had been especially ordered to target and destroy him specifically, as the potential single greatest threat to all life on Earth.

However, she had merely been drained of her life energy during the intense battle to the point that she was now physically extremely aged, and secretly chose to abandon Nate rather than let him see her in such a condition.

However, during their time apart, Threnody had fully evolved into a mutant death-goddess, constantly pursued by "zomboids", and with no desire to reform despite Nate's devotion to saving her.

[30] After the defeat of this evil "Queen Jean", Nate set out to make a difference in the world and considered himself a Mutant Shaman, a teaching he embraced from the alternate version of himself.

[32] Finally, he confronted the Anti-Man, an alien sent to Earth to inseminate his genetic code into all living cells on the planet so that his people could harvest the resulting energy.

Norman Osborn sends his team of X-Men, consisting of Mimic, Weapon Omega, Dark Beast and Mystique, to investigate and to raise public opinion.

As Norman's X-Men investigate, both Mimic and Omega are overwhelmed with Nate's energies and go on a rampage leaving Mystique and Dark Beast alone with a patient that they were examining.

After an accidental side trip to Hell the team journeys to the Nordic Hel to aid the goddess Hela against the Serpent's undead soldiers.

[49] When the X-Men and Avengers went to war over how to handle the Phoenix Force, Nate fought bravely on the front lines; first to protect Hope Summers and then to defend Cyclops' utopian rule.

[50][51] When Moonstar joined the superhero team, the Defenders, Nate remained close to her and the pair finally confirmed their relationship status when they awkwardly ran into Dani's former flame, Cannonball.

[52] Nate Grey's whereabouts are presently obscure, but Matthew Rosenberg has confirmed that he is backpacking through Europe on a soul-searching journey in response to a fan's comments on Twitter.

[60] By using the Life Seed he possessed, Nate Grey created hope out of thin air and secretly took the X-Men to this new plane of existence where everyone is a mutant and no longer persecuted for being different.

At one point a fissure opens, revealing a scene from the Prime Universe with Cyclops, Havok, Mirage and Mystique squaring off against Office of National Emergency soldiers.

[61] The Omega Machine, designed by Dark Beast, greatly diminished Nate's once incredible psychic powers including telepathy, precognition, and telekinesis.

[62] His telekinesis was so powerful that he could move massive objects with his mind, fire blasts of psychokinetic energy that could shatter steel, create mental barriers that could stop most attacks, levitate his body, and fly at supersonic speeds.

After his brief return from his dimensional travels that equipped him with a special genetic dampener that would eventually prevent his powers from killing him, Nate displayed further abilities, which included the power to view and traverse higher planes of existence, to reconstitute his body from astral energy in a similar manner as Onslaught and to transform his physical body back into astral energy.

He can capture and humiliate Apocalypse; turn off Kitty Pryde's powers; control Omega-level mutants like Magneto and Storm, turning them into his Horsemen of Salvation; telepathically communicate with everyone on Earth; wipe out all places of worship on Earth with a thought; overpower Legion in Legion's own mind and take over his body; and create a new reality where everyone is a mutant, and then transport people to that reality against their will.

Finally, Cable possesses extensive military and weapons skills as a result of being raised in a war torn future ruled by Apocalypse, while Nate primarily relies on his considerable mutant powers.

He told X-Man that the Queen tried to use his powers, but failed, and began traveling to different realities, in search of the perfect weapon, a "working Nate Grey".

When Captain America attempted to stop him, disaster struck and in addition to Xavier, Magneto, and Legion, thousands of innocent civilians died, resulting in countless new alternate timelines that Apocalypse would also rule.