Complete Monster: Masque, a Team Rocket agent who specializes in using hypnotic powers to strip Pokémon of their identities and make them his willing servants, is the true Big Bad. While initially presented as an ambiguous figure in the story and somewhat Affably Evil, he is gradually revealed to be a sick, twisted individual who enjoys the amount of control his mind games give him over others. He takes pleasure in stripping Pokémon of their identities and secretly manipulates all the higher-ups of Team Rocket for fun. He later breaks away from Team Rocket and attacks the hometown of the protagonists. While he does have an ulterior motive, it's still clear that he takes a disgusting amount of pleasure in terrorizing and slaughtering the residents of the small town with his Pokémon. When one of the protagonists call him out on his manipulations and accuses him of viewing humans as nothing more than tools, he responds thusly:
I don't see human beings as tools. That distinction is reserved for Pokémon. No, I see people more as... toys. There's a distinct difference, you see. A tool is used to accomplish something, while a toy is just there to be played with. I wasn't using Giovanni for anything other than my own amusement. And like any toy, he eventually stopped being entertaining—and when a toy bores you, there's only one thing to do: snap it in half and throw it in the garbage. That's it, end of story.
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 Crowning Moment of Heartwarming.
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.
Crowning Moment of Heartwarming: 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 B.S.O.D..
Ensemble Dark Horse: Masque, so much that when the author announced a sequel, some fans were clamouring for him to return despite him being a horrible Complete Monster who was killed off at the end. To be fair, he had developed such a considerable fanbase thanks to being a hugely entertaining Faux Affably EvilWild Card that it's not really a surprise it managed to withstand him crossing the Moral Event Horizon.
The incredible amount of entries on this page pertaining to this one character should give you an idea of how popular he is. In fact he actually isn't that prevalent of a character as you'd think from the sheer amount of tropes dedicated to him. At least, until the final chapters...
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.
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.
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.