I'll guess Vincent.

Out from the beast's heart (Hojo)
with him along,
engineering comes in handy (Hojo genetically re-engineers him)
to win.
meeting "him" again (meeting Vincent)
after raiding the lost "ark", (you fight Lost Number)
and also the closet, (the closet in the basement)
A dear and lost friend,
and a friend from your home. (former Turks - Midgar, or, you find him in Nibelheim)

I have several other guesses too - Dyne, Seto... it's pretty open, and a bit ambiguous from what I see so far.