Shredder is the main villain of the 2012 Teenage Mutant Ninja Turtles series before becoming Super Shredder.
In the series, Shredder leads the Foot Clan and maintains a long-running feud with Splinter and the turtles. His conflict with Splinter is tied to their shared history and to the rivalry between the Foot and the Hamato family.
Later in the series, Shredder undergoes a mutation that transforms him into the more powerful Super Shredder. This is a story development, not a separate unrelated villain replacing him. The character remains the same central antagonist through the transformation.
Other enemies, including the Kraang, Tiger Claw, Baxter Stockman, and the Rat King, have important roles in the 2012 continuity. They do not replace Shredder as the series’ principal Foot Clan villain during its major early conflict.