Animorphism: One of the main characters gets turned into a Pokémon in the first chapter. The main conflict for most of the story is her attempts to deal with the change and her quest to find a way back to normal. Coming back home does not, by itself, help. She finally learns that she can only return to her previous form by dying. She ends up in a state of near death but is hospitalised and lives. As a result, Missy mostly regains her human form, but several traits from her Pokémon body carry over, which she finds herself happy with.
Arch-Enemy: Near the end of the fanfic, the Scyther tends to regard Missy as his. It's unclear whether she returns the "favor".
Asshole Victim: Giovanni. It took until the final chapters for Masque to finally lose the goodwill he received from the readerbase for killing him.
A Storm Is Coming: Given the title, this sort of situation was bound to happen sometime. That sometime happens to be the final chapters, when Masque invades the real world. True to form, it leads straight into a Battle in the Rain.
Big Damn Heroes: Dan's Pokémon: despite being weakened in a recent encounter with Masque, they resolve to stop as many of the two dozen Pokémon Masque has released from killing people as possible. They save all the potential victims in the scenes they arrive at.
Deconstruction: Of the handheld Pokémon games. Many of the games' features are examined or analyzed; the six-Pokémon rule is given an explanation, for example. Dan also engages in some Navel Gazing in the earlier chapters.
Even Evil Has Standards: Giovanni has a strong interest in human culture as seen when he criticises the heroes for damaging the ruins underneath Saffron City. He also seems to show horror when he finally glimpses the true depths of Masque's madness, right before Masque murders him.
Of course, the terror he displays is less because Masque is crazy and evil and more because he's about to get murdered and he knows it.
Failure Knight: Nightshade and Artemis feel this way for failing to protect their trainer, but especially Nightshade, since the two of them grew up together and were best friends.
Faux Affably Evil: Masque is so eloquent, melodramatic, and occasionally downright funny its easy to forget that he's a completely unsympathetic, hateful bastard. At least until the final chapters, when he shows his true colors.
The Hero: Missy, naturally. (The author even said, during a Q&A time, that Dan was a Decoy Protagonist in the early chapters including the opening, and that Missy herself is the story's main protagonist).
Said Scyther has his scythe cracked and broken in battle with Missy. He's initially angry about this, but later comes to appreciate it for making him more unique, and for making the scythe sharper and deadlier as a result.
Guile Hero: Missy herself. All of her defeats over the Scyther (and a good deal of her other victories as well) basically revolve around exploiting or tricking an opponent into doing themselves in. Of course, given that she's not actually a Pokémon, this is probably her best option in taking on the world.
He Is Not My Crush: Missy denies having any feelings for Dan in the early couple of chapters. She's not fooling anyone.
Hidden Depths: Many people - so many characters give off a very specific air of personality type, only to show more complexity, either through character development or through traits we just haven't seen yet. For instance:
Luke comes off as a typical teen genius, but we later learn that his invention at the start, which robbed him of his sister and best friend, sent him into a state of grief and regret.
Ruby appears to be just a Jerkass, but by the end of the fic she's warmed to Missy enough that she finally brings down the Scyther in retribution to him harming Missy, and even tells Missy that she'd believed her story from the start (it's unclear if she was being honest, as she believed Missy to be dying) while desperately trying to wake her after the Scyther dealt her near-mortal wounds.
Hoist by His Own Petard: Masque is slaughtered by his own loyal Scyther while it's in a worked-up frenzy courtesy of Missy, and when he meets Death himself, he is terrified to see himself for the monster he always was.
Team Rocket agent Rico takes the cake, as he seems to simply exist to be an asshole. Turns out it's all a Jerkass Façade to hide his Pokémon League affiliation.
Jerkass Façade: Rico plays this so well - including actually capturing Missy in a Poké Ball when he learns Dan doesn't own her - that it was quite a shock to learn he was actually a mole in Team Rocket and a fairly decent guy. He later apologised to Dan for his actions.
Kansas City Shuffle: Masque uses one when he allows himself to be imprisoned. He has his Hypno hypnotize the guards into releasing him and then has it wipe their memories so that they forget he was there. Thereby allowing him to move around freely while everyone thinks he's imprisoned.
Karmic Death: Masque, having Mind Raped many Pokémon into losing their sense of self and becoming his servants, ends up accidently killed by the one he probably considered his finest work. The Aerodactyl's death is also fitting - trying to slaughter defenceless schoolchildren, he is utimately inpaled on the broken monkeybars at his chosen site and bleeds out to death.
The sheer style with which Masque managed to pull it off certainly didn't hurt either.
Of course, it's not so much who he'd just murdered that counts, but the fact that he'd killed a defenceless man brutally, and in the process revealed just how little it affected him. The audience was just lucky that it wasn't a more sympathetic character who'd died.
The Leader: Dan is a Type II for his group, Giovanni tries to be a Type IV but comes across as more of a type III for Team Rocket, and Masque is a Type I/IV hybrid for the end of the story.
Lovable Coward: Nemo. Subverted in that he shows signs of great courage when he needs to, and along with Missy, has the best Crowning Moments throughout the story.
Like a Son to Me: Blaine says this word-for-word to Dan - he allows him to keep searching for a way home because he doesn't want to "deprive another father of a son", but assures Dan that he's welcome to stay on Cinnabar Island if he never finds a way back home. Dan is notably touched by the gesture.
Manipulative Bastard: Masque's greatest achievements come from his ability to read and manipulate other people as well as Pokémon. In his finest moments (his murder of Giovanni and the way he busts out of prison he borders on magnificence.
Mind Rape: In a sense, this is also Masque's special ability - though it's tied to his emotions rather than to the mind.
More Than Mind Control: Sabrina is shown to have deep insecurities regarding herself and her friendship with Erika, which Team Rocket exploits to take control of her. Unfortunately for Team Rocket, it doesn't stick.
Motor Mouth: Artemis, even when she's exhausted. She's grown out of this by the time of the sequel.
Nice Guy: Armor has a bit of a temper, but when he's calm he's the most level-headed member of Dan's team and one of the best friends you can have. Beautifully ironic, considering he's a Muk and one of the least-liked Pokémon species. Dan, Missy and Artemis also count.
No-Holds-Barred Beatdown: Dan delivers one when Rico has captured Missy - he only relents when Rico gives him the Poké Ball.
Not Quite Back to Normal: Missy. This is treated as a good thing because becoming completely human would have required her to die.
Official Couple: Missy and Dan. They Do, eventually, but according to the Author's Notes, Dan first had to overcome the weirdness of having raised her as a Pokémon for a while. They actually broke up before going to university, and got back together in their mid-twenties.
Oh Crap: The collective response of the protagonists and the readers at the end of Chapter 20, when Masque and his Scyther follow Missy and Dan back to their homes.
Pokémon Speak: The reason why Missy can't explain her situation to the humans.
Ragtag Bunch of Misfits: Dan's Pokémon team give off this vibe. A human-girl-turned-Eevee (Missy/Storm), a somewhat comical but loyal Muk (Armor), a high-and-mighty Ponyta (Ruby), a timid but courageous Seadra (Nemo), a cynical Oddish (Nightshade), and a hyper Electabuzz (Artemis). Yeah ... and you thought Ash sometimes caught the weirdest Pokémon.
Rule of Symbolism: Is Masque—with his strange speech, strange mannerisms, and even stranger dress—completely at odds with the Pokémon world as we see it? Yeah. Why do we accept his presence in the story so readily? Well...see Fridge Brilliance.
Sliding Scale of Idealism Versus Cynicism: As Dan grows to better understand the realism in the world of Pokémon, he begins to realise how dark it is. The story edges even further towards cynical for much of the plot, with people and Pokémon actually DYING along the way. In the end, however, it becomes an Earn Your Happy Ending}} and all the main characters survive.
Scyther: You know, I would tell you to not bother, that by overexerting yourself with a wound like that you could very likely keel over from exhaustion, except that I don't care and I'd love to see you suffer. I hate your type, little Ponyta, do you know that? All your talk about training and practice and striving to be the best day after day after day...hah! All that training was for one reason only: to hide your shameful weakness. You started off weak, you little meal! It took quite a bit of effort to reach where you are now. Whereas I-I was born strong. Before my first birthday I had an impressive number of victories chalked up against powerful wild pokemon. Powerful pokemon; pokemon that hunted my species! I showed them that I am no prey. Before my first year passed I had killed, weakling! Killed! Human and pokemon alike! Legions of pokemon have fled from my blade. And what do you have to your name, weak one? A few victories in one-on-one battles in the safe haven humanity provides for you with their little rules? With their honor and ethics and all their safety? And even those slight triumphs were only earned after effort on your part. Do not hide what you are. The weak should not masquerade as the strong!
Later the Scyther himself gets one from Missy, it's a very epic one.
Scyther: Hide while you can, foolish one, you can't crouch there forever. And when you come out, my blade will be waiting.
Missy: How it must sting to be you, to be such a useless pokemon.
Scyther: Useless? You dare say that to me? You, who cowers beneath a shield even as we speak? You, who has never done anything but run or hide? You, who-
Missy: I know which pokemon Masque really trusts: the one he relied on to get him out of prison. The Hypno. Your master trusted him over you.
Scyther: ...That, has a remarkably simple answer. The Hypno's abilities were special-no, not special, he is not better than I am-they were just...just better suited for that particular situation.
Missy: Really? Do you honestly think you couldn't have handled it?
Missy: You know you could have, didn't you brag to me when we first met that you have killed humans and pokemon in abundance? That uncountable numbers had fled from you in terror? You could have broken in there handily, and killed Masque's oppressors before they knew what was happening. But you didn't-because Masque doesn't value you like you want him to. To him, you're just a tool, and not a particularly useful one at that. To him you're just a rusted, dull, blunt-
Scyther: Lord Masque thinks highly of me, more highly than anyone or anything else! How dare you say that? Get out from under there so I can rip you to pieces!
Missy: Masque thinks your garbage, and do you know why? Because of me. For all your claims to be invincible, for all your bragging and pride, I've beaten you twice. That's why you searched me out in this rain; not for revenge, but to prove to yourself that I'm not better than you. My victories over you eat you alive, and you know it. And even if you do kill me, even if I'm dead and gone, your damaged, imperfect blade will always be there: an eternal reminder of my triumph over you.
Masque gives one to Giovanni in a great scene that illustrates the difference between a Big Bad and a mere Wannabe. (There are a lot of these in the fic.)
Masque: Are you so shocked by murder, Giovanni? Pitiful. You are like a vulture flying high above a pack of predators, waiting to pick off whatever they leave you. You can’t kill. You’ve ordered plenty of deaths to be carried out, but you’ve never done it yourself. Any weakling can order an execution, but it takes a certain caliber to actually join the firing squad. You should have known your ambitions would attract souls much blacker than yours.
Giovanni attempts to attack Masque with his pokemon, which refuses to obey him.
Masque: Just like most of the fighters in this organization, that pokemon had been conditioned by me. Over the process I instilled a desire to serve you, to be sure, but behind that I hid something else. The pokemon of Team Rocket will never act against me…Do you remember what I once told you? ‘You cannot control a marionette with only one string’. You dared to think you controlled me?! All of your enforcers have been conditioned by me before they see use. That’s one string. You allowed terror of me to grow within your organization, so that many of your followers feared me more than you. Another string. Despite the fact that I often acted against your interests, you never took action, signaling to me and to others that I had a certain leeway out of your jurisdiction. That's a third. You never did the dirty work yourself, instead delegating it to those even more amoral than you…like myself. That’s four. I’ve made you dance this way and that for years now, Giovanni. You were my plaything. Well, now you and your organization bore me. I’ll cut your strings.
True Companions: Dan's other Pokémon become this for Missy. It's a Crowning Moment of Heartwarming when all of them, even Ruby, strive to bring her out of her Heroic BSOD. It becomes even more moving when you realise that they sacrificed their homeworld, their own sense of normalcy, and their chances of finding potential mates and having children in order to follow Dan and Missy back home, even when they don't need to. All they need now is a cheesy speech.
What Happened to the Mouse?: Read the comments on deviantART: the fandom was going nuts trying to figure out what exactly Luke was up to.
Animorphism/Baleful Polymorph: Looks set to remain a prominent theme, though not in quite the same way as it was in the first part. Instead of a human turning into a Pokémon, Armor turns into a Gallade.
All There in the Manual: The author's notes have provided something of a detailed summary for what has happened in the interim without revealing anything major about the plot.
Angst? What Angst?: In-Universe, Armor actually takes this attitude in Chapter 5. When Missy quickly becomes apologetic about his transformation, he goes so far as to chastise her because he made the choice to go through with it, fully aware of what it would entail. He is shown to have divided feelings about the situation, but is so far coping pretty well.
Apocalyptic Log: Kenneth's notes to Emily quickly become this as he starts to realize that The Trumpeter is following them.
Ascended Extra: In-universe, Rico's role compared to the last story. He's even attained a higher rank in the (New) Pokémon League.
Avenging the Villain: As of Chapter 7, we discover that Missy's life will be in danger if Alvovz ever discovers that she was responsible for his brother's death.
Gender Equals Breed: Oddly enough, averted. Although Ivan inherits some of his mother Missy's abilities, his Pokémon form is a Vulpix instead of a Growlithe, like his father Dan would have become (according to some of the various possibilities the Hypno showed Missy whilst subjecting her to Mind Rape.
Grey and Gray Morality: The (New) Pokémon League vs. The Guilds appears to be one of these, as of Chapter 5. Word of God confirms that each side is biased towards another and has left certain details of their various explanations out.
Heroes Prefer Swords: Alvovz sure does. Justified as he comes from a culture that appears to be similar to real-world Amish: eschewing more modern things, including weaponry, he took up swordplay to defend himself.
Hypercompetent Sidekick: Emily is theoretically in charge of the little excursion to Ipde, but being all of ten, Ripple is more or less really running things.
I Just Want to Be Normal: Not a straight example, but Missy has been struggling to keep too many people from learning about her... unique condition. She left university after two years to return to Fox Creek because she was having to work even harder to hide than she had to in her hometown.
The Juggernaut: In its first appearance, the Feraligatr received several minutes of off-screen punishment from Ripple and Dulcet, then picked a fight with Artemis, Nemo, and Ivan, who were eventually joined by Ripple and Dulcet. Even five against one, including one with a type advantage, they had to resort to knocking him off a cliff to win—an action that didn't even cause him to faint.
Late-Arrival Spoiler: Missy returns to her human form albeit with several Pokémon traits still remaining.
The Leader: For their respective groups, Missy is a Type IV and Ripple is a Type I.
The Medic: Dulcet, being an Audino, acts like this in combat.
Reasonable Authority Figure: Most of the Fox Creek town council (save the current mayor). Bertrand deserves special mention - he openly confesses to hating Pokémon because his teenage daughter was a casualty of Masque's attack, but he's not incapable of empathising with Missy when her son is kidnapped and agrees to her proposition. Missy even notes that he usually opposes her on principle.
Older and Wiser: Everyone's getting this to some degree, but Artemis in particular has really calmed down over the years. Nemo is this of the more self-confident variety, and Ruby looks to be considerably calmer.
Pokémon Speak: While mostly averted due to the large focus on the Pokémon themselves, Missy does use it (intentionally) when explaining that she was Storm.
Posthumous Character: Dan's father (in the "Real World"), Blaine in the Pokémon world, and of course the characters that died in the first fic.
Sadistic Choice: When they've had Luke rebuild his special machine to return to the Pokémon world, Missy is afraid of touching it because she'd rather not become an Eevee again. Dan offers to do so, but Missy tells him that he himself might become a Pokémon just as she saw while Mind Raped by the Hypno. This is promptly subverted - see Take a Third Option, below.
The Sociopath: In Chapter 7, we learn the backstory of Masque (or rather, Mugann, Alvovz's brother). According to Alvovz, he was disturbed and unstable even as a child, and developed a sickening pleasure in Mind Rape of Pokémon from a young age with his special ability.
The Strategist: Ripple has a number of pre-configured battle plans she likes to utilize in combat.
Take a Third Option: Missy and Dan aren't sure how return to the Pokémon world without risking Animorphism again, on either of them. Armor pretty much says "to Hell with this" and offers to touch the sphere which'll transport them himself, since he's already a Pokémon and wouldn't suffer nearly the same existential angst Missy did.
Retcon: The Gentle Darkness guild was originally planned to be named Ebony Darkness, but the name was changed prior to the fic's beginning due to the original name's similarity to a character from another fanfic.