Tomoya gets in an accident and has a head injury.
Tomoya loses his memory and constantly reloses his memories about once a week.
Tomoyo stays by him the whole time, with frequent rape and I love you, please remember me stuff.
Tomoya then goes into surgery to fix his problem, it doesn't go well and he falls into a comma.
Then after they both die they meet in heaven, and live for the rest of eternity happily together.