The United States military is the most highly-trained and well-outfitted military force in the world, and the soldiers assigned to Alpha Protocol are among the finest. It is notable that many are chosen more for their loyalty, patriotism, and (preferably) lack of family ties instead of solely combat experience.
The first line of defense in the Alpha Protocol facility is the US Military's Alpha Protocol Agents. Agents are dressed in Mark 2 Tech armor for added protection (resistant to everything except head shots), and typically armed with assault rifles, explosive grenades, and a wide variety of gadgets to flush enemies out of cover. They follow orders without hesitation, and many of them are used to going on field exercises with either Darcy or Westridge, with the two handlers providing top-down support and guidance from a high vantage point (much like Darcy's gadget orientation).
Alpha Protocol Specialists are also US Military and armed much like agents, but have heavier armor and helmets. Like agents, they are familiar with the Sound Generator device... and have added gadgets in their helmets to allow them to pick up sounds easier, making stealthing past them difficult. They are trained hand to hand combatants (with at least as much experience with martial arts as the agents), so any attacker should be on guard against a counter if there is any hand-to-hand attempts to take them down.