John Silver is the film's main antagonist, and something of an Anti-Villain (the villain's version of an anti-hero; an Anti-Hero's flaws are more prominent than their heroic qualities, while an Anti-Villain's good points are more prominent than their villainous qualities). Silver is rather greedy and cunning, having spent most of his life searching for the treasure of Captain Flint, but he has a caring side, too, and understands that friendship can be more important than treasure. He dislikes unnecessary acts of violence and cruelty, originally intending to mutiny only after the treasure was in hand, and thus, avoiding bloodshed as much as possible, and is generally honest and honorable in his piratical dealings. Nonetheless, he maintains a constant air of harsh brutality and deceptiveness around his crewmates, understandably necessary to maintain his position as their leader.
Based on Long John Silver from the original novel, he is a cyborg: part machine, part organic. His alien form resembles a cross between some sort of bear and man (and robot), identified as the alien species Ursid, though they never mention this in the movie itself. He has a cyborg arm, leg, ear and eye from some unknown incident, though he mentions when asked by Jim that "You give up a few things, chasing a dream.", so presumably they were lost in his search for Treasure Planet. His cyborg arm serves many purposes, such as cooking implements, a sword, a pistol and welding tool, and his cyborg eye has zoom functions and improves his aim, while his mechanical leg appears to contain an addition that he can put on his arm's mechanics to create a low-grade plasma cannon.
Initially, Captain Amelia assigns him as the ship's cook, and gives him the task of looking after Jim Hawkins. At first, they don't get along; Jim suspects Silver of being the cyborg who torched his mother's inn, and Silver doesn't enjoy having to look after Jim, concerned that he may get wind of the plans. He decides to give Jim so much work that he won't notice any plotting. However, as the journey passes and Silver gets to know how strong-willed and determined Jim is, they form a father-son relationship.
When Jim's confidence is dashed after Mr, Arrow, the first mate, falls into a black hole, Silver realizes that it must have been Scroop who did it, and tries to comfort Jim, convincing him not to give up.
However, soon after, Silver had to tell his mutinous crew that he saw Jim as nothing more than a "nose-wiping little whelp" to keep them in line, and Jim hears this just as they arrive on Treasure Planet itself. When Jim escaped with the map, he could not bring himself to shoot him. He later apologized and offered Jim a deal on the treasure, his deal appearing genuine, but grew angry when Jim turned him down, and threatened to blast him to kingdom come, although he was also shown to not wish to do this.
Later, Silver captured Captain Amelia and Dr. Doppler, and took the map, and Jim along with it. When Silver finally got the treasure, Treasure Planet began to self-destruct, and Jim almost fell to his death. Silver had to choose between some of the treasure, or saving Jim. He chose Jim, which effectively saved his life as between them, they built a solar-surfer and Jim managed to save the entire remaining crew from destruction.
Silver then attempted to escape the consequences of prison for his actions, but Jim caught him. They exchanged a heart-warming goodbye, and Silver also gave Jim his pet shape-shifter, Morph, to have Jim remember Silver by. Just before Silver left, he gave Jim the few gems he had managed to salvage from Treasure Planet, enough for Jim to rebuild the Benbow Inn. At the very end of the film, Jim looks up to the clouds and remembers John Silver, and the star/cyborg eye twinkles.
- Cybernetics - Silver is a cyborg (cybernetic organism), his right arm, leg, and eye replaced with cybernetic prosthetics and enhancements, all of which contain a myriad of functions.
- Cybernetic Arm - Silver's cyborg arm serves a variety of functions, containing a surprising amount of tools as well as weapons, such as a clamp, a sword, a plasma flintlock pistol, a torch/flamethrower, a plethora of sharp implements and tools, like scissors, a cleaver, cooking wares, etc., pincer-esque appendages, and more.
- Cybernetic Peg Leg - Silver's cyborg leg works via hydraulic pump, so damage to it inhibits him, leaving him to limp until it can be repaired. It also carries a detachable grenade launcher Silver can attach to his cyborg arm.
- Cyborg Eye - Silver's eye gives him several optic visionary functions he can use simultaneously, such as Zoom-in, Thermal vision, Night vision, X-Ray, and more.
- Cooking - Silver is a master chef and maximizes his cooking skills with his cybernetic tools, enabling him to cook his dishes at a surprising rate of speed
- (first lines) "Why, Mr. Arrow, sir! Brigin' such fine-lookin' distinguished gents to brace my humble galley? Had I known, I'd have tucked in me shirt."
- "Say hello to Mr. Mop and Mrs. Bucket!"
- "From now on I'm not letting you out of me sight"
- "You won't so much as eat, sleep or scratch your BUM without my say-so."
- "Now, you listen to me, James Hawkins. You got the making's of greatness in ya! But you gotta take the helm and chart your own course! Stick to it, no matter the squall! And when the time comes you get the chance to really test the cut of your sails, and show what you're made of, well, I hope I'm there, catching some of the light comin' off ya that day."
- (to Scroop) "I say what's to say. Disobey my orders again like that stunt ya pulled with Mr. Arrow, and so help me, you'll be JOINING HIM!"
- (saying goodbye to Jim) "Ha-ha! Jimbo! When have I ever done otherwise?!"
- The alien species name "Ursid" is very clever, as it is derived from the Latin word for bear "Ursus", but it is also the name of a meteor shower.
- Unlike the original Treasure Island (Disney's first live-action film ever) film and the Muppet version, this version of Silver is the only incarnation of the character that is not the main antagonist of any adaptation of the Robert Louis Stevenson novel at all. Instead, the main antagonist of this version of the story is now Scroop.
- Silver was originally going to return in the cancelled sequel film Treasure Planet 2, where he would be revealed to have given up on being a pirate and wanting to live a life of good from then on, and comes back to help Jim, Amelia, Doppler, and their friends defend their galaxy from a villain named Ironbeard, who would have been voiced by Willem Dafoe.
- Silver is very similar to the infamous Star Wars villain Anakin Skywalker, more famously known as Darth Vader, as both are notorious spacefaring villains who develop a soft side for the protagonist and even becoming a father figure to them, causing them to gradually seek redemption. The main difference is that Jim Hawkins has no familial ties to him beyond that, while Vader actually IS Luke Skywalker's father.
- John Silver was animated using both 2d animation and Cel-shaded CG!. CGI was used to animate his cybernetic components.