Combat is a major part of Alpha Protocol's gameplay. The player is able to decide how to approach combat. There are many ways to engage hostiles during every mission, the player can also choose to avoid combat altogether and use stealth to avoid enemies. There are in game situations where Michael Thorton must engage in combat, mainly during boss fights.
Enemies are susceptible to stealth takedowns when Mike is sneaking up on them from behind, when they are unalert (walking with their guns down or when they are suspicious but still unalert) or when they are temporarily stunned by a flashbang or shock trap. This will allow Mike to take them down instantly. This is true of the common guards and enemy faction members along with sub bosses such as Dmitri, Lazo, or the Triad leaders. This can be done as long as the enemies are not aware that Mike is there or cannot do anything in response; this can even be done facing the enemy if quick enough to avoid changing their alertness. Mike will be given the option to “Perform Takedown” or “Perform Kill”. Activating either will have Mike perform one of a variety of actions.
- Mike will strike the enemy in the throat and render them unconcious (if facing the enemy).
- Mike will kick in the hostile in the abdomen, manuever himself around the individual and throw them down to the ground (if behind them).
- Mike will throw his arm around the enemy's neck and apply pressure to their carotid artery, rendering them unconcious (if behind the enemy).
- Mike will intercept and elbow thrust to his face, grab the enemy's head and pulled it back, and then karate chop its throat. (if facing the side of the enemy).
- Mike will draw his karambit knife and stab the hooking tip into the enemy's jugular vein, pulling the blade back and cutting their neck as he lets them fall back (when behind the enemy).
- Mike will quickly pull his knife and stab the hooking tip into the enemy's jugular vein, walking forward and cutting through their neck with his hooked blade (if facing the enemy).
Mike has various weapons available to him, useful against common enemies, sub bosses and the bosses. There is a choice of the multi-tactical pistol, the blazing submachine gun, the power packed shotgun, and the fine tuned assault rifle. There is also the option of using gadgets as a main weapon, taking down enemies with grenades and traps. The pistol is useful for stealth as a silencer can be equipped. The SMG can be used to take on hoards of enemies but has poor accuracy. The shotgun is good for getting up close to enemies and taking them out quickly. The assault rifle is good for long range shooting and for suppressing sudden attacks.
Mike can use his skills in martial arts to face enemies, sub bosses and bosses. Using his knowledge of Kenpo karate, Mike can non lethally beat hostiles into unconcioussness. With a proficient skill level, the character can take on bosses as well; facing them in up close combat. Each boss character has a unique method of fighting up close except the last boss, who always relies on a powerful heavy weapon: Henry Leland and Yancy Westridge (a rocket launcher and a machine gun turret respectively).
- Konstantin Brayko will attack with his balisong knife in a frenzy.
- Conrad Marburg will use his pistol at a distance but will utilize his kickboxing skills when engaged in a hand-to-hand fight.
- Omen Deng will use stealth and a shotgun, also engaging Mike in hand-to-hand combat utilizing his knowledge of Chinese kung fu.
- Brayko is very difficult to fight up close and it is advisable to use a weapon in addition to martial arts.