Right, here goes...
The helicopter will be heavily guarded and you really don't want anyone to know it's been tampered with or the flight will be called off. So you need to place guards and patrols in such a way that the player can get close to the helo without causing an alert, but only with difficulty. If the player has to kill any guards he will need to dispose of the bodies in the time-honoured way to avoid discovery.
I would suggest patrols outside the base who may call for backup if they spot or are attacked by the player (check the editor's depot for a few scripts that will handle this). Once inside, stick the helo in a hangar. Now it gets more tricky because if the player is spotted near the helo, the flight gets called off and it's game over. If the player does well with the outer patrols, leave the base on low level alert - if the player was spotted, make it harder.
The player sneaks in to the hangar, only to discover some resistance(??) dudes planting a bomb. He is forced to fight them, which, of course, triggers an alert - the player then has to plant the tracker and escape. Meanwhile, the guards discover the bomb and disarm it, but miss the tracker.
If the player decides to disarm the bomb, he'll have to do it under fire and will not have much chance of success - he has to think laterally to realise that the guards will do it for him.
Hope that helps,
Ade