First of all, the world is made up of two gigantic titans that everyone lives on. Machines live on one, living beings live on the other. The plot begins with the hero seeking revenge for the machines killing his childhood friend/ implied potential love interest, and getting the reality bending sword from his mentor, and being able to control it effortlessly, which is a surprise to everyone.
Ok, after a great plot leading up about a war against machines, finding out that the whole war is actually due to a cycle of revenge and fear STARTED BY THE GOD OF YOUR OWN SIDE who tried to murder the entire machine race (he was the one who started the titan war in the intro), who was then sealed away, until you released him but he then died...Oh, and the sorta-girlfriend from the beginning is alive and is now a cyborg with the soul of the machine goddess in her.
It comes to a climax where you confront the leader of the machine guys, he hijacks the gigantic titan the machine people are living on to try to murder everyone living on your titan, and the hero has the perfect opportunity to finish him off for good.....and he doesn't. He instead chooses to extend the hand of friendship and end the cycle of revenge, even though that's what set him off on his journey to begin with, and it looks like this is going to be the end of our epic conclusion...
...and then everything goes batshit bonkers.
An ally you had from the start who seemed to know a bit too much KILLS the hero, releasing the God of the living titan that was sealed inside him, since he's a secret disciple of that god. See, the hero was basically a kid who had the God sealed into him as a child when his family of archeologists discovered the sword with the power to rewrite reality. The "god" that was killed earlier was only his original physical body, while his mind was sealed into the hero's body. So now the living-God comes out, announces he will now purge all life, machine and living, and restart his world to his liking. He and the machine goddess fight, she sacrifices herself to delay him, but he still blows up the entire machine titan, and reverting all the elf people on the living titan into their natural form of creepy, mindless psionic dragons (except the handful that had enough human DNA to overrride that, including your elf party member), and finally runs off with both YOUR reality bending God Sword, and the Machine Goddesses' God Sword, which basically allows him to do ANYTHING HE WANTS.
Then, the main character eventually wakes back up, the machine people give him a replica reality bending sword that functions a lot like the old one. You then kill off each of his disciples, enter his little dimension, which looks like our solar system, with the same planets and names for them, you fight him, the hero suddenly through force of his own will, gains his OWN God Sword, earning the right to be a God, and kills the Living God.
Then, you find out that the whole plot started with Earth as we know it, with a pair of scientists and an AI, who were worried that space travel would be bad for humanity, and one of the scientists basically forcibly rebooted the entire universe with an experiment. Then, he and the scientist that was trying to stop him become the living god and machine god, respectively, and the AI becomes a neutral god that was just observing everything, and was in fact a secondary character who was following you around knowing too much the entire time and being a bit suspicious. The living god then got a god complex and decided to keep wiping out all life to prevent space travel from happening. 0_o.
Hero then chooses to give up his God Sword and let the world expand. BAM, suddenly, the world is a lot larger, with continents and stuff, and the girlfriend is now human again, and the AI guy tells him to be ready to meet new species and stuff.
0_o I was staring at the screen weirded out for a while. I mean, a lot of that came out of nowhere.
Still a fantastic game, though. If they hadn't dragged out the ending with overly strong monsters, not enough properly levelled side quests to level up if you were too weak, and too many arbitrary roadblocks in the last 2 dungeons, then it would have been my favourite RPG of all time.