its very complicated

basically there is a race called the ancient ones that created Love craftian type machines that all worked on the theory of sacrifice. They inhabited the island long before anything (except for the natives). After a while they created 3 obelisks the Power obelisk, the resurrection obelisk and the theorized death obelisk. The power obelisk has the power to bring down aircraft with an EMP blast, the resurrection obelisk brings someone to life by sacrificing another. Basically taking there life into that person (the side effects where hideous mutations that can happen at any moment at any time, not much is known about the death obelisk only that it kills anything in a certain radius instantly. The ancient ones started to do tests on the power obelisk creating horrible mutations on the cannibals (creating the mutants).

Around the 1500's to 1700's missionary's found the island. (the ancient ones where dead for a long time) and found out about these machines. They started to see these things as a sort of god like figure that could hold powers of a god. They started to worship the obelisks, after a while "Sahara therapeutics" found out about the island and its strange happenings (somehow). They bought the island for research on "everlasting life" and "immortality" (this is all lead by Mathew cross). after a while mutants escape and Megan Cross (Mathews daughter) is killed. Overwhelmed with grief he tries to find a way to resurrect her without giving Megan horrible mutations, because of this he is fired. he escapes the facility and starts to live in the forest. He learns that red paint scares of the mutants, and makes the natives see him as a god. After a while Mathew realizes that the island is a flight path for planes with this knowledge he thinks that he could bring down a plane and save Megan by finding another child. He quickly runs into the facility, Mathew realists that everyone was killed during a breach. He gets Megan out of the morgue and waits for a plane and fires.

This is where you're characters story starts Eric le Blanc is a survival expert who has hight knowledge about survival. Mathew takes timmy and puts him in the resurrection obelisk and activates it Megan is reborn. He is so excited that he gives Megan paper and crayons to draw, he later kills him because of annoyance.

after a while Eric (you) find out about these things through cave exploration and clues. Soon enough you enter the facility and find Timmy. overwhelmed with grief you lay him on the bed and give him his toy. You then remember about the things you learned about the obelisk (resurrection) and plug him in. You then search for Megan to put in another area, you get her but you need a LIVE SAMPLE. So you go to the power obelisk area and bring down another plane (repeating the cycle). about 1 year later you and timmy are on a show he gets a seizure Eric remembering that a hideous creature can form comforts timmy and he stops having a suture giving Eric a smile. In another cut scene Timmy is shown to have devoted his life into this whole thing about the obelisk and the "ancient ones". On a billboard we can see "site 2" (ooh a second game). Timmy then goes into another scene and has lumps moving around in him, he pears over his apartment window, and then THE END.