For those not willing to read Ryan's long (but well-written) post, I will summarize.
Jedi Masters meet on Dantooine. They try to cut you off from the force, Kreia kills them.
Handmaiden becomes Jedi, Atris later tries to kill her.
Atris has been tainted by the darkside, you can kill her or let her be killed by the Sith holocrons.
All of your friends = future jedi, who will lay the groundwork for the Jedi of the coming generations.
Carth and Bastila are alive. They talk to you before you go to the final planet, Malachor V, the site of the Mandalorian War battle that stripped you of the force and left the force with a mortal wound.
Kreia = Darth Traya. Stop arguing that. She manipulated the whole game because you are the one one who can bring death to the force. She hates the force, so she hopes she can break you and kill it.
Darth Nihilus is a pushover. Because you are a hole in the force, he tries to devour you and ends up eating part of himself. Visas unmasks him, but you do not get to see his face.
Darth Sion learns the error of his ways before he dies.
Mandalore is Canderous.
