Last time we closed in on Karajan he sicked Kelly on us and got away in his chopper. Rather than face that possibility again it is time for Mark to get to the chopper first and ensure it isn't going anywhere.
This level also introduces a challenging new foe, the elite guard, one who is immune to stealth kills unless first disabled. Really inconvenient unless you have been upgrading your distraction items or ninja tools. Fortunately the game also provides us with some handy tools within the level itself to help dispose of some of them and as for the rest of them? Karajan probably should have invested in some gas masks for these guys shouldn't he?