I'm having trouble with the Garcia quest also (playing on the PC). Here is the order of my events:

I saved Angus, led him back to the docks.

I talked with Valdez and the conversation revelas that Garcia = Corrientes

I then talk to the remote shaman who gives me the Blood of the Ancients

I then confront Garcia/Corrientes and a fight breaks out. I kill everyone under Garcia's command, including, Garcia (at the time I thought this was all part of the normal game). The natives are NOT offended and continue to talk with me. I now have all 4 artificats needed to kill Mara.

I make my way past the fire door using the blood of the ancients, into the Hidden Valley, and into the water temple to be greeted by… a big fat nothing. Nothing happens at this point. I get on youtube and find a video where a Let's Play shows Garcia waiting there for you… ugh I think I'm screwed…

I've spent about 2 hours talking to every NPC in the game, on every island to be sure that I simply haven't missed a step somewhere. But despite that effort, I continue to have no main quest to follow and cannot travel to the isle of the dead. Any of you have any ideas?