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Break the Cutie: Jim gets hit with this hard. He goes from being a genuinely upbeat, cute kid to a brooding teenager because of the way his father abandoned him. There's also the fact that he regularly has trouble with the law, isn't doing very well in school, wants to make his mom proud...
Brilliant but Lazy: He's pretty good at building things and figuring out mechanical stuff, but at the start of the film he only uses that to amuse himself.
Byronic Hero: Melancholic, sullen, attractive (the fans seem to think so), sensitive, surprisingly cunning, and cynical. He may be young, but he's a good qualifier for it. Over time some of his more negative personality traits simmer down.
Celibate Hero: He doesn't have any romantic interest during the entire movie.
Character Development: Jim goes from the moody, sullen, rule-breaking Emo Teen, who only uses his smarts for his own amusement to a military cadet who is more happy and smiling, and learns not to be so angsty.
Crouching Moron, Hidden Badass: Jim is a lot smarter and pragmatic than most give him credit for. Over the course of the movie, he learns to curb his impulsive tendencies and think more logically.
The first is after the supernova incident, when Jim is convinced that he was the one who murdered Mr. Arrow, he barks at Silver about how badly he screwed up. It's one of the more beautiful scenes in the movie, and marks a character shift for Jim.
The second is when he learns Silver was actually a treacherous pirate all along - he tries his damnedest not to cry and then as Silver leaves the room to check out the threshold of Treasure Planet, Jim quietly stumbles around the room with a heartbroken, shocked expression on his face.
Sensitive Guy and Manly Man: The Manly Man to B.E.N.'s and Doppler's Sensitive Guy. Although, he's only really a "manly man" in comparison to those two. In general, he's actually quite vulnerable, probably even more so than them.
Also the Sensitive Guy to Silver's Manly Man.
The Stoic: Hardly shows any emotion, except the usual teenage angst. He starts to change over time.
Break the Cutie: A rare adult version, but let's look at what she had to go through: Her troubles with raising Jim, the Inn burning down to the ground, and a flashback shows her weeping when Jim's father leaving his family. Seeing this woman so broken is heartwrenching. She got better though.
Broken Bird: A flashback of Jim's showed his mother just breaking down in tears after his father left them. Combine that scene with what happened in the beginning and you'll know she qualifies.
Glamorous Single Mother: Averted. She is not a single mother by choice (her husband just left straight up left her, for God's sake) and she struggles with her restaurant to get by. Possibly played straight at the end, though.
He Is Not My Son's Father: She is horrified that the robot guards assume Delbert Doppler is Jim's father, accidentally insulting Delbert quite a bit.
Parents as People: She tries to do her best for Jim, but is overworked and likely still emotionally hurt by his father abandoning them.
Doctor Doppler: "Dang it, Jim!I'm an astronomer, not a doctor! I mean, I am a Doctor, but I'm not that kind of doctor... I have a doctorate... it's not the same thing. You can't help people with a doctorate. You just sit there and you're useless!"
Adaptational Heroism: Long John Silver of Treasure Island was very charismatic and managed to make all the heroic characters like him even as they distrusted the rest of the crew, but ultimately he was a murderous pirate who only cared for himself and the treasure. Here, he forms a genuine bond with Jim, as opposed to the empty flattery and lies he feeds him in the book, and ultimately sacrifices what's left of the treasure to save Jim's life.
Adaptation Name Change: He's never referred to as anything other than "Silver", and is never confirmed to have the "Long-John" moniker he had in the original novel.
Affably Evil: Never loses his affable nature, even after revealing himself as the villain.
Anti-Villain: No doubt he's a villain, but no doubt he cares a lot about Jim.
Last Name Basis: Though supplementary materials do refer to him as "John Silver", he's only ever referred to by his last name in the actual movie. It's easy to get the impression that he has Only One Name.
Love Redeems: His paternal love for Jim causes him to give up the treasure he's been searching for possibly his entire life just so the boy will live.
A Man and His Morph: Silver found Morph in one of his adventures and they've been close ever since. Until Silver asks Morph to stay with Jim; a reminder of the close bond between Jim and Silver.
Minored in Asskicking: Though he is the ship's chef, his leg is a damned howitzer and his arm can blow apart doors with a single shot.
Mysterious Past: Jim asks how Silver got the mechanical cyborg limbs of his body, to which Silver replies: "You give up a few things, chasing a dream." The event is never mentioned again, but it's enough to make one wonder... what exactly happened to Silver?
Noble Demon: His morals are loose, but there's no doubt that his concern for Jim is genuine. It's especially proven in the climax.
Obfuscating Stupidity: While at first glance he's an affable, outgoing chef, in reality he is a cold and ruthless pirate captain.
Though by the ending he seems to have softened a little bit.
"I say we kill 'em all now." Voiced by: Michael Wincott
Ax-Crazy: Scroop's described as a "spider psycho." The fact that he attempts to kill almost everyone he comes across (and succeeds with Mr. Arrow) shows that.
Big Bad Wannabe: Although he is also part of Silver's mutiny, he's more evil and seems to be a completely different kind of threat. But he never makes it to the treasure as he stays behind on the ship when they reach Treasure Planet and ultimately dies well before the climax.
Decomposite Character: While he is rather clearly based off of "Israel Hands", a similarly unhinged pirate from the original novel there actually is a different crew member on the ship named "Hands" (though his name is never spoken in the film).
Foil: To Jim as both have a serious disregard for authority. The difference being that Jim has a conscience and wants to be a better person. Scroop, on the other hand, is a murderous rogue, who kills Mr. Arrow, simply for telling him off and clearly isn't too keen on taking orders from Silver either.
Hero Killer: Just one look at him and the audience knows he'll turn out to be a dangerous enemy. Proves this by murdering Mr. Arrow.
Karmic Death: Just like Mr. Arrow, he gets sucked into space!
The Starscream: He would be this to Silver, except he never gets through with it before he dies. He never succeeds in doing anything Silver wouldn't want him to do other than kill Mr. Arrow, and it's not like that did anything to his plans.
Bigger Bad: Of a sort. He was a fearsome pirate, and it's his treasure (and the lengths he went to in order to keep it) that drives the plot. After Silver reforms, Flint is the closest thing the movie has to a main antagonist due to the reveal that he set the planet to explode when the treasure is found.
Greed: Flint is so greedy that he never spent his pirate loot, aside from the cost of rigging his lair to destroy whoever tried to take said loot.
No MacGuffin, No Winner: Apparently, he had this attitude toward his treasure. Rather than allow anyone else to get their hands on it (even with Flint himself long dead), he rigged the entire planet to explode if anyone entered the treasure chamber.
Posthumous Character: By the time of the story, he's long-dead. Finding his skeleton in the treasure chamber proves this beyond any doubt.