Kid Hero: Though he's supposedly at least 13, given he's identified as "an unknown teen" at one point. However, the reporter was probably just guessing.
Vague Age: He's identified as a teen in one transmission, but on the other hand, in link battles he's shorter than the other game protagonists, who are supposed to be around 11 years old.
Jovi
Michael's little sister, who helps out with an errand early in the game.
Kidnapped Scientist: Gets abducted by Cipher early in the game. They want him to use his knowledge to help them with their Shadow Pokémon plan. However, he makes it clear that he has zero interest in doing so.
Unlucky Childhood Friend: It is mentioned by an NPC that when Lily was still a student, she was very popular. Many tried to woo her, including Krane, but Michael's father obviously ended up with her.
Antagonists
Shadow Lugia
The ultimate Shadow Pokémon, and the first one created that is supposedly immune to purification. It is the key component in Cipher's plan for world domination.
Breath Weapon: Shadow Blast, which is the Shadow version of normal Lugia's exclusive move, Aeroblast.
Obviously Evil: Unlike "regular" Shadow Pokémon, which are visually indistinguishable from normal Pokémon aside from a dark aura which is invisible to the naked eye, you can tell this one's corrupted just by looking at it.
Defeat Means Friendship: Upon defeating her post-game in the colosseum, she writes you a letter saying she likes you now and makes you a part of her fan club.
Ditzy Genius: She doesn't come across as very intelligent, but she isn't the head researcher for nothing.
Expy: Fills Ein's role as a character, but with Venus's battle strategy.
His ultimate goal is to be Governor of Orre via Team Cipher. Also, he's the Straw Loser for the Cipher Admins. His strategy in battle goes from attrition damage from Shadow Sky to spamming Explosion.
Defeat Means Friendship: Upon defeating him post-game in Orre Colosseum, he writes you a letter saying that he'll be glad to make you his head secretary when he becomes governor.
Evil Feels Good: In addition to revenge, his main reason for sticking with Cipher even after his criminal behavior is exposed.
An eccentric scientist who lives in the middle of a dark forest. Most of his inventions are either useless (i.e. the Poké Pole) or harmful (i.e. the Unhealthy Sandals).
Chekhov's Gun: His scrapped Robo Kyogre invention, which Michael later uses to reach Citadark Isle, making it one Kaminko's few inventions that's actually useful.
Ardos is one of Mr Verich's two bodyguards. He is first met at Gateon Port, where he curbstomps Zook with his level 44 Alakazam. At the end of the game he is revealed one of Greevil's sons. He goes Laughing Mad after Greevil's defeat and claims he'll restart the evil organization.
Villainous Rescue: He fights Zook for the player at the beginning of the game. According to him, he was simply trying to teach him a lesson about using Shadow Pokémon in public.
Eldes is Mr. Verich's other bodyguard. Just like Ardos, he's one of Greevil's sons. However, unlike Ardos, he's not too enthusiastic about the whole "Cipher" thing. After Greevil's defeat, he pulls a Heel Face Turn and convinces Greevil to give up.