During boot camp training, Shephard is apparently trained as a sharpshooter, as he only receives advanced training on the use of the Desert Eagle and the M40A1 sniper rifle.
Shephard and Freeman do cross paths during the game, but at that point Shephard is merely an observer to a climactic event from the original game.
Shephard deactivates the thermonuclear warhead brought in by the Black Ops, but the G-Man reactivates it and Black Mesa is destroyed.
Shephard is sent into the huge underground Black Mesa Research Facility on an undisclosed mission, but things go wrong and he finds himself fighting for survival against sinister government agents and monstrous aliens.
Shephard uses explosives to destroy the creature and leaves the area through the dam's exposed water pipes.
AdrianShephard seems to have some affection for the creature as well, stroking it fondly during one of the idle animations.