The Hero — A human who wakes up on the shore to find he/she has been mysteriously transformed into a Pokemon, with no memory of how or why... or much of anything beyond their own name. As if that wasn't strange enough, he/she quickly learns that he/she also possesses a strange power that gives them brief visions of various events... It's revealed at the end of the game that the one responsible for the hero's transformation and memory loss was Darkrai.
Amnesiac Hero: Just like in the last game, the player character is amnesiac.
Baleful Polymorph: The reason for the player's transformation into a Pokemon is only revealed late in the postgame, when Darkrai reveals how he attacked (and nearly killed) them during the Time Travel.
Heroic Mime: Similar to Red and Blue Rescue Team, the player is privy to their own Inner Monologue, but aside from responses to dialogue trees, has no scripted dialogue of their own; whenever the player says something, it's a nearby NPC who responds and parrots it to the audience.
The player does, however, get to speak some actual dialogue during the game's ending, when they say good-bye to the partner right before disappearing from time. They also announce the species of the visiting pokemon during the Sentry Mini-Game.
After completing the game, if the player is present on the active team but not the designated leader, talking to them in a dungeon yields only Visible Silence instead of the randomly-chosen responses associated with other Mons.
Terminator Twosome: He/she and Grovyle were both sent back in time to prevent the Bad Future from developing. Dusknoir was sent back to prevent this.
The Partner — A young Pokemon who dreams of becoming a great explorer... but is too intimidated to join the local guild. After meeting the hero, he/she decides to try signing up as a team, reasoning that his/her new friend will help them learn how to be brave. Treasures a small rock with a strange design on it, which he/she named a 'Relic Fragment'; someday, he/she hopes to discover just where it came from...
Break the Cutie: From the Plot Twist onwards. Your hero is a liar and works for the bad guy, you're stuck in a Crapsack World and about to be executed, you have no one to count on other than your best friend and a criminal, and you have no idea of how to get home. And when you do get home, you only have a couple of days to save the world, several of your comrades have made Heroic Sacrifices to get you this far, you have to fight a Physical God, and, oh yeah, your best friend Disappears into Light right in front of you. Is it any wonder they break down crying at the end?
Everything Darkrai does to them after the main plot resolves.
Character Development: Starts out as very timid and easily intimidated, but gradually grows over the course of his/her many adventures with the hero.
Hero-Worshipper: They greatly admire Dusknoir and highly respect him. When they learn from Grovyle that Dusknoir is evil and wants them gone, they refuse to believe him at first even after Dusknoir nearly had them executed.
Kirk Summation: Uses one on Dusknoir after falling for his trap in Sky.
Messiah Creep: He starts off as a villain willing to kill the Lake Guardians and the player Team even when it won't make a difference, then is gradually revealed as more heroic. In his episode, he's regarded as an idealist and manages to talk his opposite number into reforming.
Terminator Twosome: He and the hero form a two-on-one variant, with Dusknoir opposing them.
Members of the Wigglytuff Guild
Guildmaster Wigglytuff — Guildmaster of the Wigglytuff Guild. Relentlessly cheerful and upbeat, he hardly seems to fit his fearsome reputation... yet almost everyone deeply respects him.
Chatot — Wigglytuff's right hand bird and head of intelligence, Chatot handles most of the day-to-day details of running the guild. Unfortunately, he has a tendency to grossly overestimate his own talents, and isn't as well-respected as he thinks he is...
Horrible Judge of Character: When the player and partner try to join the Guild as an exploration team, Chatot's first reaction is to kick them out for being salespeople.
Jerk with a Heart of Gold: Best shown when he starts to chew out the player and partner over the infamous Perfect Apple incident again, but almost immediately stops and apologizes. And then there's his actions in Brine Cave...
Know-Nothing Know-It-All: He describes himself as an "encyclopedia" of knowledge, and he is actually pretty knowledgeable about various legends and Pokemon (which is more or less your Required Secondary Powers for being the guild's personal Exposition Fairy), but he is also really lacking in patience and basic common sense.
Bidoof — A cheerful beaver Pokemon who's eager to please others. Before the newcomers arrived, he was the Guild's most recent recruit, and was having trouble adjusting. Things get better for him after your arrival, and he quickly befriends the team. While he can be a bit slow at times, he tries his hardest and dislikes the thought of giving up.
Nightmare Retardant: In an in-universe example, he accidentally ruins the whole "Grandmaster Of All Things Bad" setup. The Grandmaster tries to salvage it, with slight success.
The Unfought: He doesn't participate in the Grand Master of All Things Bad battle, unlike the rest of the guild.
Sunflora — A playful and skilled apprentice who's always so excited she can't help screaming with anticipation! Gets along well with everyone... well, except for Loudred, anyway... Voiced by Rachael Lillis in the dub.
Catch Phrase/Verbal Tic: "Eek!" and especially "Oh my gosh!" Her special episode is named after the latter, and for a very good reason. note She says "Oh my gosh!" 29 times in said episode, excluding two seen in flashbacks and one single use of "gosh".
Badass in Distress: During her Special Episode; Justified as she's stated to be very skilled, but goes on a solo mission with major type disadvantages against opponents who are fully aware of the type mismatch and skilled at luring others into ambushes.
Loudred — A loud and short-tempered apprentice who tends to shout all the time, and serves as the guild's morning alarm clock. Because of this, he comes off as a bit... harsh. Also a bit of a braggart, he's convinced that he's the strongest of all the apprentices.
Belligerent Sexual Tension: Explicitly acted out in Sunflora's Special Episode, right down to the "I'm not here because I care or anything" blatant lie.
Big Damn Heroes: Arrives just in time to help Sunflora out during her mission to catch the Invincible Haunter. Twice, even.
Leeroy Jenkins: In Bidoof's Wish, his AI isn't programmed to take into account Bidoof's IQ skills or Treasure Bag. Due to this, he can accidentally one-hit-KO Bidoof with Earthquake. This also happens in the Grand Master of All Things Bad battle, with the exact same allies as the special episode, minus Bidoof. Apparently, he hasn't learned.
Willfully Weak: It's said that he's already skilled enough to graduate from the guild, but chooses not to because he doesn't want to leave his swap cauldron, which is permanently stuck to the floor of the guild's quarters.
The Unfought: While Zubat and Koffing act as the the first bosses, Skuntank prefers dirty tricks and running away, and the heroes never get to fight Skuntank. Except when they take a solid one upside the chin due to a combination of The Worf Effect and the fact they're fighting the Bonus Boss.
Warm-Up Boss: Koffing and Zubat are the first bosses in the game.
Team Charm — A famous trio of all-female explorers that appears primarily during the epilogue arc. Lopunny is the leader, traveling with her best friends Medicham and Gardevoir. Their exploits are well-known, and they have plenty of adoring fans.
Even The Girls Want Them - Among the guild members gushing over Team Charm, the female Sunflora and Chimecho were just as gushy as their fellow male guildmates (with the exception of Croagunk, who seems rather oblivious).
The hero and/or partner would qualify if either/both of them are female
Fan Boys: Implied to make up the vast majority of their fan club. And the vast majority of your own guild.
The Pollyanna: Lopunny maintains a constant optimistic bliss regardless of the conflicts she and the team face.
Team AWD — An Arbok, Weavile and Drapion who are always searching for greater challenges and treasures. Lady Weavile is the team's no-nonsense leader.
Ascended Extra: In the main game, their only purpose is to advertise the Zero Isle dungeons. They become plot relevant in Sky's Team Charm episode.
Dark Is Not Evil: Double subverted in Sky, where you're told that they're a team of ruffians that will hurt others in their attempts to get treasure... and then find out that the incident you were told of was a lie by the guardian of the area to get you two to fight each other and take enough damage that neither of you would find the cave's treasure.
Team Ebony — A Shuppet and Murkrow. While both want to go searching for treasures, they can't seem to agree on what type they should target — Murkrow wants to go after the shiniest treasures, while her partner Shuppet prefers rarity to sparkliness.
Team Flame — As the name implies, a Fire-focused team; two of the three members, Ponyta and Camerupt, are Fire-types. The leader, Bellsprout, is a Grass-type, which means he's on the wrong side of Elemental Rock-Paper-Scissors. Despite this, he tries to be a good commander, and his teammates care deeply about him.
Team Razor Wind — Zangoose, Sandslash and Scyther make up this team, which derives its name from their speed and razor-sharp claws. Notably appeared in the first anime special, and had a very brief cameo in the second.
The Worf Effect: Their Cameo in the first Time/Darkness anime adaptation was simply to demonstrate Wigglytuff's strength by having him whup their tails offscreen, as well as Gabite's by having him do the same.
The Kecleon Brothers — A pair of Kecleon who run the local Item Shop. The green one handles regular items while the purple one specializes in TMs and Orbs. Always changing their inventory.
Badass Bystander: Should you provoke them in a Dungeon Shop, you'll find that they're level 49, with max stats and permanently at double speed. Playing this trope more straight, it is possible under very rare circumstances for them to begin fighting the wild Pokemon alongside you, without actually joining your team, should a wild use Explosion or some other attack that damages their goods.
Xatu — Runs "Xatu Appraisal"; he uses his strange abilities to see into sealed chests before opening them (which he immediately does afterwards, as that's the service he offers). Speaks in an overly grandiose fashion.
Marowak — The new head of the local Dojo, which was forced to close down for lack of customers some time ago. As such, he's almost painfully eager for any new customers to show up and start using the faculties. These courses aren't as harrowing or punishing as normal mystery dungeons (primarily in that there's no penalty for defeat), so they're great for training.
Lovable Coward: He has an obsessive fear of the hardest maze in his own dojo. To the point that he sealed it off.
Azurill and Marill — Two cute youngsters. Despite their youth, they're both very responsible and polite, running errands for their mother and staying out of trouble... or, at least, not actively looking for trouble.
Teddiursa and Ursaring — Usually found hanging out together, these two villagers are always ready to weigh in with their thoughts on the latest news. Teddiursa eventually chooses to evolve, making telling them apart a bit difficult.
Spinda — Opens a Cafe in Sky which provides extra services and is all about "hopes and dreams~" Can be a bit... loopy at times, but he's good at mixing drinks, and gives others a place to run their own new businesses. How they stay in business is anyone's guess...
My Significance Sense Is Tingling: While he can't control when it happens, Spinda will always sense whenever the drink he's just created is special somehow and warn the customer.
Wynaut and Wobbuffet — These two help Spinda by running the Recycling Station, which doubles as the Lottery and the heart of 'Project P'.
Cannot Spit It Out: While normally Wobbuffet responds to Wynaut's questions about whether or not a given ticket is a winner, sometimes she goes very quiet. This can signify that it's a big win... or that she's just reluctant to admit it didn't win anyway.
Verbal Tic: Wynaut tends to phrase things in a way that he can ask "why not" or "is it not?" Wobbuffet, meanwhile, hardly says anything other than "That's right!" or announcing what color you just picked.
Dusknoir - A very wise explorer who rose to stardom overnight. Despite this, he's very humble and willing to help even the smallest Pokemon. He's from the future, where he's Primal Dialga's right-hand Ghost-type.
Dark Is Not Evil: ZigZagged. He is introduced as heroic, but is then revealed to be villainous. In the fifth Special Episode, he seemingly pulls a Heel-Face Turn, only for it to have been fake all along, but then he pulls a realHeel-Face Turn right then and there, which sticks.
Heel-Face Revolving Door: Appears to be good at first, but then reveals he's Primal Dialga's right hand man. Then in the special episode in Explorers of the Sky, he comes to a truce with Grovyle only to reveal later that he faked betraying Primal Dialga. Shortly afterward, he finally settles on a side, and makes a genuine Heel-Face Turn.
Leitmotif: "The Power of Darkness" as well as his own boss theme, "Battle Against Dusknoir".
Pet the Dog: Coming to the party's rescue in Amp Plains becomes this in hindsight, as as far as he knew at the time, the Player and Partner's well-being were inconsequential to his mission. Then again, he may have done it just to keep up appearances.
Pragmatic Villainy: Dusknoir's speech after being defeated at the Hidden Highlands heavily implies that all his motivation for evil stems from fear of death; as his existence is tied to the Bad Future, he will go to any lengths to keep history on its negative course. Sky version's final Special Episode confirms this to be the case in a heart-to-heart with Grovyle, and also has him overcome it and become Not Afraid to Die.
Leitmotif: "Planet's Paralysis" during cutscenes, and "Dialga's Fight to the Finish!" when finally fought - the latter appears in various forms throughout the game when time and the Time Gears are involved.
The Chessmaster: He's so well prepared for the final battle, it takes the intervention of a Physical God to stop him! Not to mention that he was the mastermind of the main plot.
Crazy-Prepared/Dangerously Genre Savvy: His original post game plot was to convince the heroes they should destroy themselves. When that didn't work, he convinces Palkia that he should destroy them. When that failed, he already had a backup plan to lure them to their deaths at his hands. When they show up, he tries to convince the player to join him by trapping them in a nightmare where their partner betrayed them and joined Darkai. When that failed, he summoned his army of Mooks to help him kill the group. Then when he lost, he had an escape route ready and would've escaped had Palkia not intervened. Yeah, he had a total of five backup plans!
Dark Is Evil: A Dark-type, and the main villain of the post-game plot.
Dark Is Not Evil: After his memory is erased, he can be recruited and turns out to be an extremely loyal ally.
Evil Cannot Comprehend Good: One of the main reasons his plans failed. He failed to factor in that The Hero could still be...well, heroic after losing their memory and didn't finish the job then and there. Another example is at the end of the game, when he tries to pull a We Can Rule Together on the hero and their partner. He makes the partner in the illusion join him out of depression, something the real partner would never do. This creates A Glitch in the Matrix that allows the hero to escape.
For the Evulz: It's never explained why he wanted to destroy the Pokémon world besides destroying both time and space in order for that to happen.
Heel-Face Brainwashing: After he loses his memory, you can find him wandering aimlessly through certain dungeons, and can eventually recruit him.
Nice Job Fixing It, Villain: The heroes had no idea that he was distorting space. They only find out when he tries to kill them, allowing them to stop his plans. Justified as he knew that when his nightmare would start spreading, the heroes would begin to find out why. And with the player's Dimensional Scream, figuring out who was behind it could become really easy.
Obviously Evil: As soon as you see him for the first time, you know this is not the Woobie Darkrai from the anime.
Omnicidal Maniac: It's not directly stated, but given the impact of his plan, it's fairly obvious.
Pink Girl, Blue Boy: Invoked: the plot-relevant Celebi is Shiny note in the main series, shiny Celebi cannot be obtained, but a shiny color is coded in for it as a legacy from Generation II, meaning she's pink rather than green.
Big Damn Heroes: Just as it appears that Darkrai is about to get away by escaping through a dimensional hole, Palkia shows up and attacks Darkrai as he begins to time travel. This causes Darkrai to lose his memories the same way that he caused the player character to lose his/her memories at the beginning of the game.
Dungeon Bypass: Being the god of space allows him to go wherever he pleases; his last IQ skill allows him to move through walls, tearing them down.
Hero Antagonist: He only fights you because he thinks you are the one who distorted space when it was actually Darkrai.
Incoming Ham: "I HAVE FOUND YOU AT LAST! THE DEFILERS WHO ARE CAUSING... THE DISTORTION OF SPACE!"