I like the story. It's touching, and nicely paced.
The game could use a few more improving touches, but it's nice as it is.
It really needs a soundtrack, which you could pick up from the pool of free to use music here on Newgrounds. I suggest two or three themes to go with the change of moods as the scenes change.
A quick return system, to go back & forth between decision points and not have to click through already known scenes, would certainly make the exploration of the variation more enjoyable, by removing the tedious frantic clicking interruptions.
Finally, a medal system, a tie-in with Ng medals, or even just a checklist screen where the endings appear as they are found (perhaps associated to the key art of that ending scene) would help the users know, in game, how their exploration is progressing.
Seriously, keep it up! Once you've mastered the little polishing touches, I hope to see you do longer stories! You've obviously got a nice grasp on the pacing & storybuilding, and that's the meat & potatoes of this style of game.