The year is 2042, the stage is a huge futuristic city Neo Kobe. Among the remains of passengers who died in a plane crash, experts discovered a strange biomechanical organism. Recent events proved that it was not the only appearance of a "snatcher" -a robotic creature who can masterfully disguise itself as a human being in order to infiltrate and to destroy human society. Gillian Seed, a man who suffers from amnesia, remembers just this word: "snatcher". He joins the Junkers, a combat unit whose goal is to track down and to exterminate the snatchers, and is determined to find out the truth about those creatures and his past.

"Super Deform Snatcher" is based on the same story as the more famous Snatcher, but gameplay-wise it is an entirely different game: a role-playing adventure. You navigate your hero from top-down view, enter buildings and talk to people. In many locations you'll meet enemies who are visible on the screen. Upon contact with an enemy, a turn-based battle begins. You can choose to fire from a variety of weapons, and to target a specific part of the enemy's body. Targeting has a direct effect in battles: for example, shooting the enemy's gun will weaken it, destroying its wheels will prevent it from avoiding your shots to its face or body, etc. You gain experience points ("rank points"), improving in different categories (speed, defense, etc.). You also improve your weapon skills by continuously using the same weapon.

Unlike "Snatcher" with its "serious" graphics, the characters in "Super Deform Snatcher" have a typically Japanese animé "super-deformed" style, which adds an element of a parody to the game.

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