A mutant, better known in some circles as the Incredible Nightcrawler, was captured by a mysterious government agency, but escaped into New York. Once there, he secreted away in a church, only to find he wasn't the only one using it. Tinkerbell, a member of the Brotherhood, invaded his sanctuary as her own, and the two began to talk. Meanwhile, at the prompting of Professor Charles Xavier, three X-Men, Cyclops, Eclipse, and Gambit, set off to locate and assist the escaped mutant picked up by Cerebro. Once there, they were involved in a brief but fortunately non-violent confrontation with Tinkerbell, and the sudden appearance of Nightcrawler shocked Gambit into memories of his encounter with the Morlocks. The psychic impressions were picked up by his teammate, Eclipse, giving her the clues to his darkest secret.

Ultimately, the X-Men successfully recruited Nightcrawler and headed back to report in. Gambit and Eclipse later met up to discuss what she had seen in his mind. She promised to keep his secret, and also told him a little about her life with her mother in California, before her mother died and she discovered that Charles Xavier was her father, information she usually kept closely guarded. The conversation strengthened their connection, and, unbeknownst to Gambit, Eclipse's attraction to him.

Eclipse was quickly pulled away from the mansion, sent on a mission alone to rescue another lost mutant, Chameleon¹. She arrived at the girl's hotel room to invite her back to the mansion, but was interrupted, first by thugs sent by Chameleon's father to kill his daughter, and then by Magneto, who made short work of the previous threat, but presented an even greater one himself. Magneto had come to size up the young Xavier, and to drop a tantelizing hint at his next move. One word: Huitzilopochtli, the name of an Aztec god. His trap baited, he left them, but Xavier had located him in the area and sent Gambit and Rogue to help Eclipse, interrupting a date between the stormy couple. They arrived just in time to rescue Eclipse and Chameleon from the regrouped thugs. Unhappy to have needed saving, Eclipse's gratitude was lacking, but she took Chameleon back to the mansion ("Closing Doors"). Eclipse went to the Profesor, taking up her ire about being rescued with him, and although they argued, the conversation did turn towards the clue Magneto had passed to her. Eclipse promised to follow up on it, but no progress was made in the father-daughter relationship between herself and Professor X. A short while later, Eclipse and Cycops set off to find more information about the Heart.

While Eclipse and Cyclops were away, a more personal drama played out within the walls of Greymalkin. After a run-in with life-leaching mutant, Rogue accidentally harmed Gambit with her power. While he lay unconscious in the medlab, she fled to a common refuge, Wolverine. He took her out to escape her troubles, as usual, but this time their chemistry flared into something more, and both admitted feelings for one another. While Rogue and Wolverine sorted out what to do about their new possible relationship. Gambit awoke and sought out Eclipse. Instead, young Xavier student Catalyst found him, and they talked, obliquely referencing his growing interest in Eclipse. But almost immediately aftewards, Gambit and Rogue met up again, and Rogue dropped her bombshell...she ended their long, conflicted relationship to pursue one with Wolverine.

Magneto met back with his Brotherhood, and laid out his plans to steal the Aztec artifact, the Heart of Huitzilopochtli. His stated reasons were that it endowed its user with magical abilities, but in truth it was only a step in his plan to turn Eclipse to the Brotherhood, to take Charles Xavier's daughter to replace his lost Anya. He led the Brotherhood to Earth to claim the artifact, breaking into a museum to steal it, but they were, as Magneto hoped, interrupted by Cyclops and Eclipse. The Brotherhood gained the upper hand on the two X-Men, and Magneto made off with both the Heart and Eclipse. Cyclops was left to report back to the X-Men with the news that Eclipse had been captured by the enemy Charles Xavier had been trying to protect her from all her life.

On Asteroid M, Magneto and Eclipse retired to his private chambers, where Magneto proceeded to 'educate' her on the subject of her parentage. He described not the loving relationship Eclipse had always hoped her parents had shared, but a younger Charles Xavier, on the rebound after his relationship ended with Moira MacTaggert, beginning a reckless affair with Eclipse's besotted mother. Eclipse, who'd always been fearful that this was the truth Charles's silence on the subject had concealed, believed too easily. Magneto exploited her rage, making her the target of the almost-sentient Heart. On Earth, the X-Men marshalled their forces for a rescue, but Magneto transmitted down that he would be willing to return Eclipse unharmed, at a neutral meeting place. Before Magneto could gather her up, Eclipse finally made contact with the Heart. The mystical artifact of the Aztecs imbued her with the spirit of their warrior god, and his need for destruction and chaos. Its prisoner and instrument, she attacked Magneto, and stole a shuttle from the Asteroid, heading to Earth to kill Charles Xavier, and make way for the wars Magneto would begin after his death, a mission quite beyond the scope of what Magneto had intended. His plan had gone wildly awry. As Eclipse headed to Earth, Magneto and the Brotherhood gave chase, Magneto secretly hoping to stop her rampage.

The X-Men arrived at the predetermined coordinates, a deserted oil field in Texas. A Brotherhood ship touched down, and they readied for a battle with Magneto, but only Eclipse appeared. She attacked quickly, using her power in ways she'd not yet dreamed of, forcing her teammates to fight against her. Though her own reserves of energy were rapidly draining, she managed to seriously injure the almost-indestructible Rogue, and the new recruit, Angel. The Brotherhood arrived, and Magneto gloated over the fallen Rogue, his former flame, while Nightcrawler had his first taste of battle as he met up with Quicksilver. But when Eclipse, with the help of Xavier, freed herself from the heart, the battle ended with the destruction of the artifact by Gambit. Magneto called the Brotherhood back; Xavier had survived and Eclipse, though unconscious and severely weakened, would not join his own daughter Anya in death. Though the Brotherhood demanded an explanation, Magneto still concealed his true motives from them.

The X-Men regrouped and returned to the mansion for recovery. Rogue was released quickly, though Angel suffered far more severe injuries. Eclipse, meanwhile, awoke to find her father waiting for her. Xavier had seen much in her mind, enough to understand this the silence between them on the subject of her mother could not go on. He showed her the truth, Eclipse's mother was not a fling, but the love of his life. Father and daughter took the first small step towards a real relationship.