What are the consequences of your decision on the plane in Deus Ex?
If you kill Lebedev
- You don't get any XP Points (!)
- Ana is pleased with your performance
- If you talk to Gunther at the helipad, you inform him that you killed Lebedev. Gunther congratulates you
- You receive a message from Alex that Manderley is pleased with your performance.
- You get 1000 credits op bonus. Manderley is happy that you followed his orders
- You will have to face Ana Navarre later on either in the subway in Battery Park after escaping Hell's Kitchen or in the Unatco HQ after you escape MJ12 prison
If you kill Navarre
- You receive 200xp points
- You get to hear the entire dialogue between JC and Lebedev (like sb mentioned, he dies after from the hands of MJ12 and you are getting blamed for it)
- Alex is freaked out by what happened but promises to erase the logs to cover for you
- If you talk to Gunther at the helipad, JC lies to him and tells him that there was a shootout at the 747. Gunther says he needs to investigate to check if Navarre is fine
- JC lies to Manderley about the 747 situation also, saying that Lebedev shot Navarre
- Gunther will discover you killed Navarre upon your escape from Unatco HQ
- You receive 1000 credits
If you don't kill neither Lebedev or Navarre - Ana kills Lebedev
- You receive 175xp points
- You get to hear most of the dialogue between JC and Lebedev
- Ana Kills Lebedev and expresses her disappointment in your performance
- If you talk to Gunther Hermann at the helipad, JC tolds him that Navarre executed Lebedev. Gunther says he will congratulate her
- Alex sends you a message upon reaching Unatco HQ, He says you shouldn't sweat it for not killing Lebedev
- Manderley is extremely pissed you didn't follow orders
- You receive 1000 credits anyways, after a short argument between JC and Manderley
Other soldiers at Unatco and general Carter will provide their comments based on your decision. Gen Carter will support your decision about not killing Lebedev (even if Ana kills him), he will be compassionate if you actually killed him, saying it must have been difficult.
In the end, Killing Navarre is the most advantageous choice - you get the most Xp and get rid of her early on. However, it is an extreme scenario in which you also loose some interaction with Navarre later on when you need to face her again and fight.
Not killing Lebedev seems the most logical, reasonable choice as it shows JC hesitant to finding his brother working for the terrorists and refusing to kill an unarmed prisoner.
Killing Lebedev is the least advantageous option as the player doens't receive any xp points. I find that very disappointing because it shows the game developers are "interfering" with your choices and punishing a player that chose to follow a difficult but direct order from his superiors. As much as I love Deus Ex, I found this quite dissatisfying that you're being "forced" to choose save or not kill Lebedev simply because those choices are more favorable.
At that point, you pretty much have to make a choice of trying to save Lebedev or killing him. If you choose to kill him, then that's that and you will have to face and fight Anna later.
If you want to save him, you will have to take out Anna.
If you choose to walk away, Anna will kill Lebedev for trying to 'escape' and you will still have to face her later.
Personally, I usually take the opportunity to take out Anna at that moment. The easiest way to do that is to slap a laser trip mine on the door frame just before you enter the room where Lebedev is. Anna will trigger it and get blown up as she enters.
However, even if you do save him, he is captured later on by MJ12 and then killed. His death will be blamed on you. You will learn of these events through the news.
Note, it is also possible to arrange a way so neither is killed, but it is very difficult and doesn't affect the story anyway.
If you don't kill Anna on the plane, you have to do it later. It's much easier then, because you'll have either a combat shotgun, plasma rifle or (best of all) the killword for her. Killing vs. not killing her has no other in-game effect; I presume that if you "save" the guy on the plane, he is later, shall we say, shot while attempting to escape.