Ass Pull: Proto Man having his pre-programmed obedience to Wily accidentally erased by the programing that removed his confidence in Episode 11. While not completely impossible, it only comes up in the narration right before Proto Man has to decide to kill Mega Man or not to give that last little push for him to change sides.
Awesome Music: Music in a fanfiction? Well, sort of. The author suggests playing WilyCastle 1 from Mega Man 2 during Rock's first raid on Skull Castle.
Growing the Beard: While the first two episodes are good, the story really hits its stride with Episode 3, exploring more emotional territory and providing its own spin on several episodes. Episodes 4 through 7 continue this by starting to tie the subplots together and introducing new takes on elements from the game.