Complete Monster: Masque is a seemingly friendly Team Rocket agent, with an innate, empathic ability that he uses to Mind Rape Pokémon, stripping their identities and making them his slaves for him to manipulate anyone he wants. Breaking away from Team Rocket, Masque has his Scyther brutally murder Giovanni by slashing him up, and later escapes police custody to slip into the protagonists' world; from there, Masque attacks their hometown with his Pokémon, commanding them to slaughter the residents for his own sadistic pleasure. Planning to continue his massacres from village to village, Masque admits that he regards people as nothing more than toys to be used and then destroyed when they no longer entertain him.
Fridge Brilliance: One of the major themes of the story is identity, particularly in the form of Missy's attempts to return to normal and come to grips with her new form as a Pokemon. What better Big Bad than Masque, a man who not only brainwashes Pokemon (thus taking away their individuality and identities) but also literally hides behind his own mask the entire story?
Growing the Beard: While the opening chapters are decent but mediocre, the story becomes much better written afterwards. For a start, the overwhelming majority of tropes come from those parts of the story.
Nightshade has been beaten to near-death by a bullying Aerodactyl, trying to protect some children and make up for what he percieves as his failure in protecting his trainer. After Artemis defeats the enemy, she comforts him - using his old name, Tuber, she reassures him that they succeeded and saved the children, and that he did well. This breaks down the wall of cynicism he'd built around his heart and he smiles before finally passing out..
At the end of the fic, everyone's come to visit Missy in hospital except for Dan. Missy calls him in, and he's so embarrassed and ashamed of himself for not knowing who she was and his treatment of her while she was a Pokemon - including making her sleep on the floor. Missy just kisses him softly, assures him that she doesn't hate him and it's alright, and falls asleep out of exhaustion - content for the first time in a long while.
Blaine telling Dan that he considers him a surrogate son and that he always has a home at Cinnebar island if he never finds his way back to Earth.
The other Pokemon all working together to break Missy out of her Heroic BSoD.
Hilarious in Hindsight: At the start of the fic, Luke is working on a machine that is supposed to play Game Boy Advance games in 3D. The Nintendo 3DS saw the release of Pokemon Omega Ruby and Alpha Sapphire, remakes of the Gen 3 Pokemon games.
Any time Missy fights the Scyther is one for her. Period.
Nemo is a Crowning character of Awesome whenever he gets to shine. Particularly notable due to his meek personality.
Missy breaks free from the Hypno's Mind Rape through sheer willpower and takes him down.
Armor defeating an Alakazam, a Pokemon with a type advantage over him.
By knocking it into a raging river and punching the shit out of it.
Ruby practically incinerating the Scyther in retribution for his almost killing Missy - after he defeated her earlier in the story. When you consider how much she disdained Missy for much of the plot, this doubles as a Heartwarming Moment.
Artemis, after being almost defeated by an Aerodactyl and saved by Nightshade, puts aside her ditzy attitude and stands her ground, attacking and ultimately killing the Aerodactyl in both defence of some children and to honour Nightshade's sacrifice.
Masque of all people gets one, when he Deconstructs Giovanni for all that he really is - a spineless bully - and then orders the Scyther to slaughter him, cementing himself as the story's trueBig Bad.
Moral Event Horizon: Masque crossed this hard when he blackmailed Luke into creating technology that would allow him to traverse worlds and create chaos for the sake of it. Arguably, he's already crossed the line when he sent his brainwashed Pokemon to slaughter innocent people in Dan and Missy's hometown indiscriminately.
Storm Clouds II
Harsher in Hindsight: In the first story, Blaine was something of a Parental Substitute to Dan and even told him he was welcome to stay on Cinnabar Island, whilst acknowledging that not letting him leave would deprive a father of his child. Cue the sequel, not only has Dan's father since passed away, but he's shaken upon discovering that Blaine succumbed to old age three years past.
Iron Woobie: Missy has since evolved into one of these, considering she's dealing with not only being different from other people, but also her nine-year-old son's recent kidnapping.
Armor, probably, as seen in Chapter 5.
Tear Jerker: The Feraligator's backstory might be this, if you're sensitive enough. Blaine having died definitely qualifies, Dan's crushed response to the news not helping matters.
