The Phoenix Force is forcefully brought from the Marvel Universe into the Ultraverse by the Alien Ship that caused all the Ultraverse's heroes to gain powers. In an effort to control the Force, the Ship severely damages it and drives it insane so the Force is forced to take a new host to recuperate. It possessed the young hero Prime, and then takes down the combined forces of the X-men and Ultraverse. When the ship tries to take over again, the two teams are able to overtake Prime and Phoenix Force leaves his body and goes to possess the Exile Amber Hunt.
The newly possessed Amber Hunt fights the X-men, Ultraforce and the newly arrived Exiles (with former x-villain Juggernaut), Night Man and Mantra. Meanwhile the Ship is kidnapping Rex Mundi and his genetic Alternate to get the source code embedded in their DNA so it can reunite with the rest of itself inside the sun using the Phoenix Force to propel the Earth to it. The combined force of heroes infiltrated the ship and rescues Rex and the Alternate, and they free the Phoenix Force from the Great Ship. As the Force attempts to kill the ship for attacking it, the heroes use the various powers to send the Phoenix through a gateway back to its home world.
In the second issue of all 1995 Malibu titles there was a 3-page flip side story. These 7 parts were a prologue to the Phoenix Resurrection storyline that followed
Prime - Prime is enjoying his adoring public when he spies Gateway in the crowd smiling at him. When Prime flies down to him he is transported to Manhattan of Earth-616 and hit by a cab. While the cabbie yells at him he sees Gateway sitting over by a tree, but mid-flight over to him, he transports back to the Ultraverse and crashes into the tree. He looks down and see the image of the Phoenix in the painted in the dirt.
Night Man - Night Man is wandering New York in the rain, pondering his new found mystical abilities when he suddenly sees, through a puddle on the ground, directly into the bedroom of Damian Hellstorm. Hellstorm at first attacks but then questions his mysterious intruder. He hypothesizes that Night Man is not an attacker but a "peeping Tom" from another world. He warns Night Man of cataclysm to come and sends a flaming sword through the portal which, upon entering the other side, becomes a blazing firebird. He warns that the Phoenix would soon be upon his world.
Siren - Whizzer of Squadron Supreme is intently analyzing data at Mt Pegasus. He ponders the dimensional breaches that have been appearing all over the place and decides to consult other in the field. After no answer from the Avengers and the Fantastic Four, he reaches Beast of the X-men. The two scientists agree to exchange data and contact each other later with more conclusions.
Mantra - Lauren Sherwood is sitting in a diner hating and revering the popular kids from her school, thinking about if only they knew she was secretly Mantra, when she noticed them looking over at her. They are staring at the little man suddenly sitting next to Lauren: Gateway. Lauren instantly apologizes for the kids and begins to pour her heart out to Gateway, who sits silently. She almost outs her secret identity but composes herself and continues her rambling. Suddenly she notices that he is gone and on the table in front of his seat is the outline of a Phoenix in salt. She gets a sudden ominous feeling about events to come.
Exiles - Amber Hunt is out on a balcony feelign incredible remorse for the recent atrocity she committed under the control of The Entity. She remembers that a small part of the Entity is still lodged within her, and as she drifts off in thought she begins to envision herself engulfed in a firebird and swears to never allows someone to make her kill again.
Rune - Rune is attacking a man who regularly and brutally attacks women when the two men are both transported to the grounds of the X-men's headquarters.He sees Storm and Beast through a window and then drags his victims body into the woods where he realizes that he is in someone else's territory. He makes note of the person's scent just as he is teleported back to his own world. And we see Wolverine sitting in shadows.
Ultraforce - Ultraforce is fighting a former KGB agent assassin named Meat Rack and in a freak occurrence Prototype and Topaz's energies mixed to and Meat Rack to Earth-616. Spider-man is alerted by his Spider sense to the arrival but Thor came by and sent him instantly back to his own world. When Meat Rack arrives back in the Ultraverse, the Black Knight wonders how the villain came be covered with newspapers from his own home world.
The Phoenix Force is flying through space and is heading back to Earth after its long travels through space. A passing rock full of technological wonder passes by and observes the Phoenix before jumping back to its own universe.
The X-men (including Storm, Beast, Wolverine, Rogue and Bishop, together with Generation X's Banshee and Jubilee are all standing in the Terrarium that serves as the training ground for Generation X. Banshee summoned them here and they soon see why: Gateway has drawn a large Phoenix symbol and all of their images (as well as a few others they don't really recognize). Suddenly Gateway teleports them away in the blink in the blink of an eye.
Meanwhile at Project Pegasus, the Squadron Supreme are watching the readings from the numerous space/time disruptions that have occurred when they see another one abruptly show up. They wonder what this object could be since it is much less then human mass. The scene cuts to the techno-rock that observed the Phoenix reentering this universe and sinking to the bottom of the sea. At the bottom of the sea, the seafloor opens up to accept the meteor and it travels through the caverns and pathways of the Great Ship. The rock unites connects to the Ship, and, as it rises to the ocean surface, it realizes it is almost complete but need a power source to reach its remaining pieces. Luckily it has just found such a power source...
In the Ultraverse Washington D.C., the X-men appear in mid air and promptly crash to the ground. Wolverine thinks the places smells wrong, similar to Night Man who he met recently, and the group deduces that they are now in the Ultraverse, where several of them have been before. They prepare for the usual downscaling of their powers when Bishop points their attention to the sun and the large black blot on it. Elsewhere, the Ship sends a beam of energy into the sky and tears a hole in space and time to Earth-616. On the other side, the Phoenix Force is unwilling dragged through the opening, as the whole scene is broadcast on national television. As Beast marvels at the majesty of the Phoenix Force, Mantra, Amber Hunt, and Night Man all see the firebird . The Ship sends an extraction beam to drain the power of the Phoenix to use for itself. The X-men are disgusted as they watch the Phoenix writhe in pain in the sky. As the Phoenix fights for its freedom, its mind begins to falter and fracture, but still it battles the Ship attempting to enter the Ships mind. The sea boils as the Ship reels from the Phoenix's attack, and the Phoenix, severely wounded, desperately searches for a host so it may heal itself.
As the X-men decide how best to help the situation, Prime arrives and says since they obviously know the entity they are just as guilty and he is arresting them. Wolverine, is his way, tries talking to Prime but Prime decks him which causes Rogue to attack. Elsewhere, Rex Mundi, the original Ultra, observes the events taking place and decides to send his agents, while in another headquarters The Alternate, Rex Mundi's female genetic counterpart, also observes the Phoenix and sends her own agents, The Solution.
The Phoenix selects and dismisses candidate after candidate from the Freex, the Strangers, Solitaire, Sludge, Necromantra...however in the middle of a pitched battle with the X-men, the Phoenix decides upon Prime for its new host. As the X-men try to decide how to handled the newly hosted Phoenix, the Brand-new Phoenix-Prime revels in his/her/its new host body and the power that comes with it. It tells the X-men to run, as it is about to turn this entire world to cinder for abusing it. Meanwhile at Headless Cross, Cromwell becomes aware of the events unfolding and alerts the rest of Ultraforce.
Back in Washington, Beast postulates that the Phoenix, like them, is operating at a reduced power level while Storm, Banshee and Rogue attack Phoenix-Prime head on to no avail. When Phoenix fries Wolverine, he jumps right out of the flames and lunges at Prime, claws out. Then the Ship decides to take control of the Phoenix, giving Prime a chance to try and expel the entity from his body. The X-men take this opportunity to pounce on Prime. On the Lower East Side of Manhattan,
Interlude: Rose Autumn is sitting home with her father watching TV when a pain suddenly shoots through her head and the Phoenix emblem appears in her eyes. She screams in pain and her fathers runs to her. They both wonder whats happening...
In Washington, Ultraforce arrives on the scene and even as the Black Knight recognizes the X-men, Topaz, Ghoul and Prototype attack the team they see ganging up on their teammate. Before the battle gets any worse, the Black Knight jumps in the middle and diffuses both teams. While Black Knight and Storm catch each other up to speed, Phoenix-Prime rises and zaps the very lifeforce from everyone present, but the Ship once again attempts to take control and Prime falls to the ground. Both teams beset the fallen possessed hero and while he makes attempts to throw them off they are too much for him. The strain of fighting the teams gives Prime the reprieve he needs to fully expel the Phoenix from his body and as he collapses he says he saw into the mind of the Phoenix and he knows what is coming and that the Phoenix is now insane. In one part of California, Lauren Sherwood becomes Mantra and travels after the firebird she saw in her vision, while in another part of California Night Man opens a door in the air and steps through after the Phoenix that Hellstorm warned him about.
Interlude: Back on the Lower East Side, Rose is staring out the window wishing she could go out, but the doctor and father says she needs to rest. She thinks about the flaming bird image she saw and wonders why it seemed so familiar. On the street, an older blond man watches her from the street.
While traveling to New York on Ultraforce's ship Black Knight asks Storm to brief Ultraforce on the Phoenix's history. She recounts the story of the space mission that ended with Jean Grey piloting a spaceship through a radiation storm and how Jean almost died until she was saved and replaced by the Phoenix. We get a quick run through of the M'Kraan story and the Dark Phoenix Saga where the false Jean died on the Moon. The conversation soon becomes a debate over can they kill the Phoenix and whether they should kill it. Ultraforce wants to kill the being whereas the X-men think it should be saved and preserved with Black Knight siding on the side of Ultraforce. Wolverine interrupts and begs the question what if it can't be killed?
On a balcony in New York City, Amber Hunt is with Cain Marko, the Juggernaut, and she tells him of her vision where the Phoenix comes for her. Rather then fight it she plans to let it take her and try to fight for control from within. She still feels responsible for the many deaths that happened while she was controlled by "The Entity" and sees this as her chance to make things right. As he tries to say he won't let that happen, she knocks him out and sees the Phoenix coming for her in the distance. Ultraforce notices that it stopped right over Manhattan and Prototype points out that it found its new host as the Phoenix-possessed Amber Hunt floats above New York.
Amber relishes in her newfound power as she descends gently from the sky. A block away Ultraforce and the X-men arrive in the scene just as Amber/Phoenix notices the arrival of Quattro and Gun Nut. Rex Mundi observes from his sanctum thinking how he should have disposed of Amber long ago. Back in New York, the Solution shows up and a fight breaks out between them and Quattro while Amber's mind travels down into the alien ships that brought the Phoenix to this world, and discovers the true goal of the ship.
In Manhattan, as Storm is wondering what is happening suddenly the X-men's old enemy the Juggernaut shows up with his team the Exiles, of whom Amber is a member. Everyone breaks into a large melee, and the Phoenix screams as the Great Ship takes control of her form. Wanting to study them for traces of the microorganisms it craved, the ship controlled Phoenix drops everyone, with Juggernaut falling last. Inside the ship, the disembodied mind of Amber Hunt watches as her body forcibly searches the minds of the leaders of Quattro and the Solution and find that their powers came from two different sources. The X-men and Ultraforce attacked together and momentarily weakens her before she knocks them all back. The X-men and Ultraforce convince the other teams to work together with them as Mantra appears on a nearby roof to join the fray and Nightman appears from a street level portal. With all the heroes working together, they get the Phoenix on the ropes.
In the nearby apartment of Autumn Rose and her father, Autumn looks out the window and sees the Phoenix firebird heading for her building. As it crashes into her building, they are sent falling to the floor below them. In a sudden show of strength, Autumn lifts a massive piece of debris off of her father, but she doesn't have time to marvel at her new power as she discovers that her father is a robot. Beast and Bishop attempt to calm her but in her agitated state she transforms into golden skinned being of energy and blasts the Phoenix before both women collapse to the ground and Autumn reverts to her human form.
As the ship only needs the Phoenix and not Amber, Amber falls to the ground as the Phoenix rips from her body and flies away. All present are stunned to watch the Phoenix split into two in midair and go off in separate directions. As the combined teams discuss splitting in two to chase the Phoenixes but Amber tells them that they would never be able to catch them but that she knows what they are doing. She tells them that if they all work together then they MAY be able to stop the ship from using the Phoenix to drive the Earth into the Sun.
She recounts the story of the Break-thru when she was possessed by the ship and Black September when it was reawakened. The ship wants to drive the Earth into the Sun to recombine with its missing parts but needs its guidance system, or pilot, in order to do this which was hidden inside the body of the first Ultra, Rex Mundi and, since her created his mate as his own genetic double, Regina, the Alternate. The ship then decided to acquire all copies of the pilot program and has sent the Phoenix Force to abduct them.
As the large group of superbeing leave Manhattan to save the world, an older blond man watches them go and then, along with Autumn robotic father and Autumn unconscious body, disappears.
Rex Mundi and the Alternate are brought to the ship by the Phoenix and then both of them are plugged into the ships techno-organic machinery. It keeps them sedate with nanotech as it rebuilds them as part of the living ship. In the lower levels of the vessel the united assemblage of Ultras mutants appear through one of Gate's portals in a wreckage yard of old planes and ships (giving an explanation for the Bermuda Triangle). As they are marveling at the sight, they are besieged by creatures acting as the ships "anti-bodies" while in the control room, the ship is downloading the pilot program piece by piece from its captives and funneling Phoenix energy into the Earth mantle. Volcanos erupt all across the world as the Great Ship revs its engines preparing to propel the Earth.
In the midst of all the fighting, Mantra notices Topaz glaring at her, but the reason for this is not revealed.
One group continues to fight the techno-organic beasts while another group breaks off to attempt to stop the ship's plan. As the second group reaches the control room door, Prime enter and is beset by more monstrosities while Amber goes to the control panel to try and stop the process. The combined voice of Rex and the Alternate telling them to stop what they are doing but after brief discussion Black Knight makes the call to destroy the machine. Wolverine does so and frees Rex and Regina, but the Phoenix, wounded and trying to reform, begins to build in power.
Across the globe, the volcanoes on the verge of eruption being to calm and settle but back in the Great Ship magma begins to pour through the tunnels of that were dug below it. Using Gate's portal and a spell from Book, the gathered heroes (including Rex and his Alternate) transport to the deck of a nearby tanker. Suddenly Shruiken cries out for everyone to look out to the sea as the water boils and the Phoenix bursts from the ocean. It hangs in the air for a moment before turning its searing energy on the Great Ship at the bottom of the ocean. They all decide that the Phoenix can't be allowed to destroy the Great Ship, lest it also destroy the world. Using Gate's portal and Amber's connection to the ship to boost its power, the rest of the heroes use their formidable powers to push the Phoenix through the gate back to its original universe...and 4 billion years in the past. It folds in on itself as it prepares to travel back to its proper place and time. In the resulting explosion from its travel vacuum, large fragments of rock are sent flying into space, to eventually intersect with a large sentient alien ship.
Back in the Ultraverse on the tanker, Rex and Quattro have abruptly and subtly departed. Regina talks about how she had hoped for better from Rex after their experience with the ship but she wasn't surprised by his departure either. Suddenly Gateway shows up on Ultraforce flying transport and all the heroes say goodbye and depart just before Gateway teleports the X-men back to their home dimension.
On the surface of the sun, if you look really closely, you can see a spot that is the remains of the great ship. It knows it will be reunited one day...just not today. But it is very patient.