Vortiguants are one of the Aliens from the planet xen that teleported to earth after the resonance cascade in HL:1. At the time they were hostile to the humans because they were being controlled by the mind of the Nihinlith (can't spell it
). After you kill the Nihilith they are released and join the hunam resistance against the Combine invaders. in Half-life episode 1 it is revealed that they might have some special purpose/power as they prevent the G-man from taking you back (cutscene at the beggining of Ep 1).
And you will definitely not be playing as a vortigaunt in episode 2, however they will fight alongside you against the various enemies.