Veteran
Upon starting the game, you must select your class. The class you choose dictates what skills receive bonuses at the beginning of the game. However, choosing the "Recruit" option gives no bonuses to any skill and, at first glance, only seems like a way to make the game more difficult. While playing as a recruit is challenging, upon beating the game and replaying it a second time you now have the option of choosing the "Veteran" class. This class gives three ranks in every skill and offers additional dialogue options through the game, making it the best class available.
Special Weapons
A limited number of special weapons exist in the game. These weapons offer higher damage compared to their counterparts, as well as a unique look. If you choose to execute Brayko, you gain access to his SMGs. Executing Omen Deng gives you his shotgun, while executing Marburg at the museum gives you access to his pistol. Sneaking up on an Al Samad Lieutenant at various points in the game gives you access to his gold-plated assault rifle.
Brilliance
As there are limited ability points in the game, it is important to plan in advance what skills you wish to acquire with them. Regardless of the class you play as, Brilliance should be one of the first skills you learn. When used, Brilliance resets the cooldown on any special ability or skill, allowing you to use that skill again instantly. Brilliance is learned in the eighth rank of the "Technical Aptitude" skill tree, with Master Brilliance being learned in the final rank. The only difference between these two is in the amount of time it takes before you can use Brilliance again: normal rank requires 240 seconds between uses, master rank requires only 45 seconds.
Chain Shot
While "Alpha Protocol" offers a variety of weapons to use, one of the best weapons is the pistol. What makes the pistol the best weapon is the Chain Shot ability. When used, this ability slows down time and lets you aim exactly where you want your bullets to land on an enemy. At master rank, Chain Shot allows you to place six shots anywhere on a target. By placing them on a target's head you can achieve maximum damage with each shot. With the master rank of this ability, most enemies, including bosses, die almost instantly when this is used. Combined with Brilliance, you can achieve 12 shots to the head in a rapid manner, which no enemy in the game, including the final boss, can withstand.