The individuals listed here always have a built-in numbers advantage due to their ability to manipulate puppets to fight alongside them. Different methods are used to control these puppets, anyone who is able to control inanimate dolls will be considered for this list regardless of whether they use magic, technology, or actual strings. The abilities of the puppet masters vary greatly, and the puppets themselves demonstrate various levels of awareness, but the characters on this list are never alone in battle.
The World Ends With You
Shiki Misaki is a fashionable girl who never parts with her homemade stuffed animal, Mr. Mew. She's a talented seamstress who makes all of her own clothes, but Mr. Mew is easily Shiki's most impressive creation. Mr. Mew looks harmless, but through Shiki's "psychomancy," the stuffed animal becomes a clawing beast that viciously attacks enemies. Shiki is able to duplicate Mr. Mew in certain situations, and can even use fusion attacks to transform him into larger, more powerful forms. Shiki's ability to animate objects only works on Mr. Mew, and her power is indirect at best. Although she gives commands, Shiki is quick to note that Mr. Mew typically does his own thing. Her skills as a puppeteer are limited compared to some of the other characters on this list, but the fact that she made Mr. Mew herself is impressive in its own right.
Carl Clover is a child prodigy who dropped out of Military school. With the help of a mechanical marionette named Nirvana, Carl travels the globe as a vigilante. Carl believes that his mysterious puppet is actually his sister, Ada. Their father had used Ada as part of an experiment, but Carl was able to escape with her in tow. Other's have trouble understanding how Ada could have been turned into a lifeless doll, but Carl never loses faith and refuses to be separated from her. Carl is reliant on his sister in battle, but he also has an emotional dependency on her. Having lost most of his family to his father's experiments, Carl develops severe trust issues and clings to whatever part of Ada still exists within Nirvana. Nirvana was never meant to see battle, but proves to be quite dangerous due to Carl's reliance on sneak attacks.
Tales of the Abyss
Tokunaga was a large puppet given to Anise as a gift from her mother. When other children became jealous of Anise, they smashed Tokunaga into dust. An elite general witnessed the vandalism and decided to fix Tokunaga in his laboratory. Tokunaga was modified to be able to connect with Anise's elemental "fonon" frequency, which ultimately allowed him to grow larger and to be used in battle. Anise enlarges Tokunaga, rides on his back, and uses telepathy to give him instructions. Tokunaga lacks speed and evasive abilities, but he's a powerful ally who gives Anise more strength than she would otherwise have. Although Anise can use both melee and magical forms of attack, she wants to be viewed as a delicate maiden who needs protection. This ultimately makes Tokunaga the perfect companion for her.
Arcana Heart Series
Known internationally as the "Crimson-Eyed Criminal," Lieselotte became a cold-hearted assassin after she was orphaned. Lieselotte is emotionally scarred to the point that she can't even recall what happened to her family. She is somehow able to carry the consciousness of her older sister, Elfriede, in a creepy, ball-jointed puppet. The two travel the world together, and Elfriede's ability to manipulate other puppets makes the duo a force to be reckoned with. Between Lieselotte's vacant expressions and Elfriede's disturbing appearance, the sisters form one of the most unsettling duos in all of gaming. Despite their wicked actions, Lieselotte ultimately has good intentions. She was unknowingly responsible for the death of her family, but she wants nothing more than to be reunited with them.
Shadow Hearts Series
Gepetto is an eccentric and lecherous old man, but his age brings wisdom and he's able to provide invaluable information on the occult. In his youth, Gepetto was a famous puppeteer in the theaters of Paris. His popularity has started to fade, but he's still renowned as a showman. Not much is known about his past, other than the fact that he had a daughter named Cornelia who died at a young age. The puppet Gepetto uses in battle is an exact replica of her and was named in her honor. Gepetto never goes anywhere without his beloved Cornelia, and channels his magic-based Marionette skills through her. By dressing Cornelia up in different outfits, Gepetto is able to make her attacks even more powerful. I'm not sure how dressing up a puppet in bondage gear is supposed to increase its fighting ability, but you can't argue with results.
Final Fantasy VII
Cait Sith is the most iconic puppeteer from Final Fantasy VII, though some might question if his stuffed moogle buddy can even be considered a puppet. Ultimately, the method in which someone controls a puppet is irrelevant. Whether they're using strings, telekensis, or (in Cait Sith's case) a giant megaphone, anyone who controls an inanimate object is fair game for this list. The giant moogle is clearly an inanimate object, but so is Cait Sith. Cait Sith is revealed to be a robotic cat that is controlled by a Shinra executive named Reeve Tuesti for the purpose of gathering intelligence. While Reeve controls Cait Sith's actions from afar, he also controls the giant moogle via Cait Sith's megaphone. In a sense, Reeve is a puppet master who uses a puppet to control a second puppet. It's like something out of a Christopher Nolan movie.
Mel is an eccentric girl who never goes anywhere without her androgynous wolf puppet, Branky. Mel is polite and courteous, but Branky is always looking for a fight. It's unclear if the doll is really alive or if Mel is merely a ventriloquist who is making the doll talk. Mel insists that Branky has a mind of its own and will even bash him against walls when he says mean things, but most people are convinced that she's just putting on a convincing show. Even though Mel is outright abusive at times, Branky is fiercely loyal to her. He's obnoxious and foul-mouthed, but he's also concerned with Mel's well-being and proves to be very protective of her. Brank's brand of humor is not for everyone, but the results are astounding when Mel uses him in battle. Branky is basically used as a glorified claw weapon, and his teeth are almost as sharp as his insults.
Super Smash Bros. Series
It's easy to forget, but the concept of the first Super Smash Bros. involved figurines fighting against each other. The Nintendo-branded toys were brought to life by Master Hand, and the stages were elaborate dioramas that were apparently created by him as well. Master Hand didn't merely control a single character. Rather, he was in control of all of the characters and the source of creation for the entire Smash Bros. universe. There is little information about Master Hand's origins, but he has acted as the final boss in every Smash Bros. game and is still seen as a symbolic link between the real world and the imaginary battlefields of Super Smash Bros.. The extent of his powers are unclear, but the fact that other characters are able to fight against him suggests that his abilities are anything but absolute.
Final Fantasy X
Lulu specializes in the art of black magic and represents an era bound by traditional beliefs. Her appearance is anything but traditional, however, and her attire was strongly influenced by fashion models. Her stoic nature makes her seem detached and insensitive at times, but she's always able to handle herself on the battlefield. In combat, Lulu makes use of various dolls to help cast powerful spells. These puppets are based around popular Final Fantasy characters like moogles and cactuar. Nobody knows how she is able to control the puppets that surround her, but they act like sentient children who view Lulu as their mother. Lulu eventually settles down and has a real child. I'm impressed that someone was able to remove the massive collection of belts she wears around her legs.
Alice made her debut as a stage boss in the third Touhou game, but she was later promoted to playable character and has become an icon for the series. Alice is a bit of a loner, and lives in the "Forest of Magic" with her self-made dolls. Despite being an all-purpose magician, she prefers to let her dolls do the fighting for her. She is able to manipulate a large number of them at the same time, and can instruct them to perform separate tasks or cooperate with each other. The dolls can also act asynchronously and are even said to be able to control other dolls! Alice often enlists the help of her dolls Shanghai and Hourai to do her chores, but she's basically doing the work herself since she has to give them commands. Her ultimate goal is to create completely autonomous dolls that would have their own thoughts and move on their own fruition.