@Lurker: Bad Lurker, no cookie.
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Ok, here's my read, and my 2 cents...
First off, I dislike Mind Control spells quite a bit. If used by the GM, they remove control from the players, which is a bad thing. I'll use it on rare occasions for story purposes in my home game, but I know my players, and I can usually do stuff like and get away with it without upsetting them. But some players really resent that sort of thing, so it should never be done by the GM in a Missions game. Not the topic at hand, I know, but...
WHen used by a player, it can really ruin a game as well. But, as I said above, all spells are subject to the "noticing spellcasting". So generally speaking, while it might get you out of a jam, it's not all that reliable because it's not stealthy in the least. He'll know what happened to him when he snaps out of it, even if he doesn't know who did it (If you're good enough at hiding yourself). That's a possible serious complication.
And as pointed out, depending on how you use it, it could completely ruin the fun for other players. This is where being a good GM comes in, and relying on the players willingness to relax and have fun playing the adventure they paid 4 bucks to play (at a convention, anyways).
First off, never kill off a player for doing something legal, by the rules. (This is why Lurker gets no cookie). Of course, in game, their actions may have consequences leading to their death. This is the risk you take when you run the shadows. But as the GM trying to steer a game and prevent it from being not fun for the other 3-7 players you may have sitting at your table, talk with the player first. Warn him that it's a bad idea, and it will have consequences. Let him know how we handle these spells (Noticing SPellcasting, negative reactions, etc). Not all GMs run it the same way, since these spells have NEVER been defined well, in any edition of Shadowrun. So be sure and let the player know what he's dealing with.
If he insists on going through with a poor action, let the other players know whats up, and see how they want to handle things. Peer Pressure can be a wonderful thing. And hey, they may just shoot the guy to prevent him from being stupid.
If, after all that, the playeer still goes through with something like Mind Controlling the Johnson... Well... Play it out. Use the bonus dice you get from Table rating for resistances and noticing. Derail the adventure, have them hunted down. Play it straight, play it fair, but if they can survive for 4 hours, let them live. If they can somehow pull off ripping off the Johnson and not having to do the run, let them. They get no karma. They don't successfully complete the adventure. They get no contacts. It's their loss. And if they really want to drop $4 a person to finish the game in 15 minutes, let them. But be sure they note this on their Debreifing sheets, and be sure to tell them to make future GMs aware of what happened. Because there may be repercussions for these actions. Characters show up again and again in Missions, and this will be even more true in Season 4.
As pointed out, Mind Control is annoying, but it's no different from someone playing stupidly uncouth, or deciding to geek the Johnson in the opening scene, or one of a thousand things players can do to wreck an adventure. The GMs job is to tell the story and try to steer the players and the action, but when a team is really determined to go off the rails, well, let them. Just keep in mind there are consequences. And make sure they know that too, and let them adjust their actions as needed.
99.9% of your players will not be an issue. Most are there to have a good time, and so long as the GM tries to put on a good show, they're generally pretty forgiving. When you have that .1% problem player... Well... It's tough, but work with it as best you can.
Bull