Metal Gear Solid
Plot twist, the man who aided you the entire time was in fact the man who murdered your mentor whom you thought was assisting you and used you to start up Metal Gear Rex. The kicker was you saw him right in plain sight several times and he played you like a damn fiddle.
Games where the final boss was visible from the start/part of the game the whole time?
Aiden Ramirez
Jackson Cook
No Kirito lost but managed to get close enough to stab him back. It was a double K.O. but bad guy let him live
Carter James
The abridged series is really good.
Dominic Harris
Is that Edelgard?