I recently completed Prototype on xbox 360, but not without quite a bit of frustration at the final boss encounter.  This frustration, however, was mainly due to my impatience at wanting to complete the Story Mode instead of spending the time to upgrade Alex Mercer to a kickass level.

My biggest recommendation is to upgrade Alex’s blade powers; something which I hadn’t done by that point and I ended up loading up an earlier save game to devote to upgrading Alex’s powers.  Once you have all of the blade powers head into that final battle with confidence!  Initially I had taken to running around and letting the military forces sort out the Supreme Hunter until he’s at the health level where you flip over into the timed 1:40 mode.  With maximum blade power, you won’t have to even bother with this cowardly tactic.

As soon as the cut scene ends, turn on Alex’s armour and blade power and lock onto the Supreme Hunter.  While locked on, alternate with your X and Y attacks – it’s here that you might need to experiment to find the right rhythm but I managed to find one where the Supreme Hunter could hardly get a hit in.  Something that I wasn’t initially aware of is that if you manage to hit the Supreme Hunter with enough successive shots he can be stunned!  It’s at this point you need to grab onto him (using the B button) – Alex will jump on top of the Supreme Hunter and it’s now that you get to go to town on him with rapid X button shots.

I found that I was able to get two stun sequences before I had to quickly consume some Military to gain extra health.  By that time the Military had depleted the Supreme Hunter’s health to a point where the final timed attack began.  Remaining armoured with the blade weapon active it should take two to three attacks to stun the Supreme Hunter before you’re ready to watch the final cut scene.

Sit back and pat yourself on the back for completing Prototype.