The story of Claymates begins when a scientist creates a formula that transforms clay into living animals. A Witch Doctor desires the formula for himself, capturing the scientist, and transforming the scientist's son Clayton into a blue ball of clay. As Clayton, the player must travel across the world, from his backyard to Japan and beyond, in order to rescue his father and return to normal.
- All There in the Manual: The backstory and the names of the characters as well the gameplay, there's all in the manual.
- Big Bad: The Witch Doctor who steals the clay formula and Clayton's father, as well converting him into a blue ball of clay.
- Blob Monster: Clayton's blue ball form.
- Claymation: As with the main series, no computer animation was involved, with all clay characters rendered from hand-made models.
- Limited Special Collector's Ultimate Edition: Some copies of the SNES box had a holofoil cover; tilt it one way to show coins representing the different animal transformations, and tilt the other for the animals themselves.
- One-Hit-Point Wonder: The default blue ball form.
- Punny Name: Clayton. Also his father, Dr. Putty.
- Shapeshifter: One of the main gimmicks is Clayton transforming into different animals using pieces of his father's formula scattered across the levels, giving him different abilities depending on the form.
- Spin-Off: Of ClayFighter series, mostly the first game.
- Take That!: The American version of the SNES box touts "Blaze Processing", that "accelerates characters to incredible speeds", a reference to SEGA's "Blast Processing".
- Unexpected Gameplay Change: Between platforming levels, the player has to complete block-moving puzzles to unlock the path forward.
- Witch Doctor: The antagonist of the game.