The search for "Pan" is on, and Lady Mastermind wants revenge. After the team (minus Cable, Cannonball and Sabretooth who are back at the Xavier Institute for Higher Learning) discover a possible location for "Pan" they follow the lead. When the team scout out through out the building, Rogue and Omega Sentinel find a teleport gate, Rogue realises that it was a setup, and she is kidnapped by the Plague Dogs who work for "Pan" (who by this time has been revealed to be an old friend of Professor X, Richard Palance).
As the others follow Rogue through the portal, Cable and Cannonball follow with Sabretooth onboard the Conquistador. They end up in Calcutta, and Iceman, Lady Mastermind and Omega Sentinel head for Pandemic's headquarters, with Mystique missing. They attack the tower, and engage the powerful Pandemic in battle, and lose. Pandemic uses his powers then to send the Conquistador flying into the upper atmosphere, and Cable fires the only weapon left on board, Sabretooth.
It's revealed the Pandemic aqquired his powers from a virus he created. He has powers from over 300 mutants, and now intends on using Rogue to create Strain-88 so he can aqquire any powers from every mutant he touches. He uses Rogue to create the virus. As the captured X-Men are about to be disected, Mystique kills Pandemic's assistant and frees the other X-Men, and they fight Pandemi as Sabretooth fights the Plague Dogs outside. Cable and Cannonball arrive and fight Pandemic's goonies, and in the end, Pandemic touches Sabretooth and his healing factor kills Strain-88 in Pandemic's body. Rogue is released and goes to kill Pandemic, but falls unconcious, and Cable reveals she's dying (Pandemic is put in a coma by Lady Mastermind, where he's constantly running through a maze)!