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Now thinking about Wolverine 2, I think probably Viper was working for Mr. Sinister? So she would have to technology to negate mutant's ability and drain them out. Maybe Sinister was trying to use that old guy for experiment, and at the same time control his corporation to support his research.

Also the computer file screen in X-2, anyone noticed the second one in the bottom was Dr. Nathaniel Essex?

http://images2.wikia.nocookie.net/__cb20100702002643/marveldatabase/images/e/ea/X2_-_Folders_on_Stryker%27s_computer.jpg