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Off My Mind: Professor X's Secret Agents

Why did he need secret agents and what other secrets is he hiding?

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We've all heard those famous words that pretty much sum up Charles Xavier, "Professor X is a jerk!" To me, from the very first time I saw him, I was creeped out a little. I'm not saying Professor X is a bad guy. He's done a lot of good things. His whole mission of trying to create a world where mutants and humans could live in harmony is something to be admired. He dedicated his life and family fortune to creating a school for gifted youngsters. He helped troubled and confused children learn to control their newfound abilities so they wouldn't hurt themselves or others. If they happened to have cool enough powers to become a member of his team of X-Men, it was an added bonus. 

But Professor X is far from an honest man. He has had so many secrets revealed and I wonder how many more he has locked away. He faked his death early on, had a secret crush on his student Jean Grey, was a deadbeat father to Legion after promising to always be there for him, manipulated Magneto's personality (which lead to the birth of Onslaught), knew the Danger Room became a sentient being and still kept it enslaved and erased Cyclops' memories of his brother Vulcan when it looked like he died on an ill-prepared mission. 

All of these are pretty bad things but what I've been thinking about is another secret he's kept for many years (no, I'm not referring to his possession of an Infinity Gem with the Illuminati). Why did Professor X employ Mystique and others before her as his secret agents
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  Agent 16 is dead.
Agent 16 is dead.
In the 2003 series, Mystique, it was revealed that Professor X had a mutant named Prudence Leighton as his secret agent sent on who knows what sort of missions. He needed agents he could send out and if they were caught or compromised, Xavier or the X-Men wouldn't get the blame. 
 
I can understand his reasoning for this but it's still a big secret to keep from those closest to him. Make that another big secret.  
 
  Shhhh.... 
Shhhh.... 

  She was the best around and no one was gonna keep her down. 
She was the best around and no one was gonna keep her down. 
Not only did Mystique become his new secret agent, he also employed another mutant, Shortpack, as her handler. Throughout the series, Mystique was sent on missions to Cuba, North Korea, Africa, Brazil and Sweden. As far as I know, this secret never really came out or was discussed. The X-Men were pissed when they found out about Cyclops sanctioning X-Force, how would they feel about Xavier using a killer/terrorist like Mystique?   
 
An argument could be that he was just using Mystique for a greater good. She was expendable. He tried getting her to use non-lethal weapons (Forge was her gadget maker) but come on, this is Mystique we're talking about. 
 
  Mystique is questioning Xavier's ethics? That's not good, Chuck. 
Mystique is questioning Xavier's ethics? That's not good, Chuck. 

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Besides just using Mystique as his secret agent, Xavier did have other agents. Prudence's field name was Agent 16. Were there at least fifteen other agents out there? There was even mention of a mutant cleaner in Germany that would take care of any messes left behind. We saw the few missions that Mystique was assigned to. What other missions did Xavier send agents on? What other secrets did he have? How long did he employ these agents? He even spoke to Mystique telepathically during other X-Men/Xavier Institute activities. This says that he could have been doing this or still be doing it. 
 
It's a cool idea. I wish we could've seen more of Xavier's secret spy organization. Maybe after working with Mystique he decided to put a stop to his secret shenanigans. The events of M-Day could have reduced the available agents or maybe he's still employing them. Who knows if we'll ever find out more about what missions he had and what information he gathered. So does this secret add another layer to him being a jerk or does it make him a little bit cooler?