Those who’ve played the first Mass Effect will find Alpha Protocol’s skill system somewhat familiar. Players can pick a class to start out with that begins the game with points invested in various skill chains or specializations, such as pistols, assault rifles, hand to hand combat and stealth. They then earn advancement points for completing various objectives during missions, and can invest further in these chains, unlocking new abilities, or diversifying into different chains.

On the surface, there is a lot of room for diversification in the various player abilities. However, in the big picture, players will find themselves developing in one of two main play styles: a straightforward shoot 'em up type, or a stealthy infiltrator type who relies on opportunistic close range sneak attacks and gadgets. Unfortunately, the game doesn't excel at making either of these approaches a particularly satisfying experience.

Superficially, Alpha Protocol is experienced as a third person shooter. It is not altogether twitch based, however. For the most part, if you aim and shoot at someone you will hit and kill them, but there are accuracy and other stat-based calculations that affect your efficiency. The player will be far more effective with weapons they specialize in. The longer they hold position and zero in on a target before firing, the more lethal the weapon will be. Gunplay, however, is rather uninspired, with enemies that aren't very challenging to mow down (with the right weapon), and a cover system that can be somewhat frustrating to use.

Stealth play is similarly lackluster, missing many of the features from successful stealth games, like the ability to hide enemy bodies so they don't alert other guards (the bodies will still alert them, you just can't do anything about it). It is also missing easy to follow cues as to how visible you are at any time, and who can see you, meaning stealth is often reduced to simple trial and error. In place of more refined features like these, players are given “invisibility” powers at higher levels, which remove any lingering traces of challenge there might have been. Sneak attacks generally consist of pressing a button from behind a guard to instantly kill or incapacitate him. In the rare event a guard turns around, hand to hand attacks consist of spamming a single key, and are relatively infallible on most minions, even at lower levels. If an alarm is tripped, most of the time the worst this means is that you simply have to dispatch the guards in the immediate area, which is easily accomplished by isolating them and picking them off with hand to hand attacks. Failing that, while pistols are generally only suited for close range sneak attacks, there are few problems in the game an assault rifle won't solve quickly, even with few ranks in the skill.

In addition, to bypass certain challenges without combat, and to unlock many perks on the map, there are a number of mini-games the player can attempt, like electronics, lockpicking and hacking. None of them are particularly fun. Lockpicking is ridiculously easy (at least in the PC version). Hacking can be somewhat frustrating, with an interface that can be difficult to read and too slow to respond to directing the code segments around the screen that you need to place. Regardless, you will be doing these minigames again and again, especially if you're trying to sneak around. Any character build can attempt the mini-games, but players who don't optimize towards this end are likely to find the time limits problematic, at least for hacking.

More physical exercises are sadly limited to various isolated “hot spots” around the game map, for the most part. Mike can crouch to move stealthily but he cannot jump, or execute any other impressive maneuver, unless he finds an opportunity to do so. This can be a little frustrating at times, such as when you have to go the long way around a wall of sandbags two feet high because you can't simply hop over, or when you have to find just the right spot to be able to jump down to a lower level. Alpha Protocol has intentions of being an action game/RPG hybrid, but Mike's limited repertoire of motion tends to limit its appeal as an action game.

With all the various means at your disposal for effectively eliminating or bypassing guards, and the pronounced weakness of the poor enemy A.I., it's difficult to summon any sense of tension in the various missions. There are few real consequences for triggering alarms, and minions are generally only dangerous in large numbers, otherwise they are fairly easy to avoid and pick off. The only real challenge, at least on the default difficulty setting, comes from various boss battles and occasional areas where one set of skills is more helpful than another. Generally, a straightforward shooter is going to be more practical for most situations in Alpha Protocol than a stealther, who may struggle at times. The game has a checkpoint save system, and save points are plentiful. In the event a player gets impatient and blunders into more than he can handle, reloads are generally painless, except for maybe having to do a few repetitive mini-games over again. The result is that it's easy to develop an apathetic air of recklessness while undertaking missions that feel monotonous before too long.