Plankton
Plakton is the evil mastermind in the movie.  He is the one behind stealing Neptune’s crown. When he takes the crown,

he sells it off and it is taken to Shell City.  At the palace where he took the crown from, he leaves a note framing Mr. Krabs. 

He does this because he has failing restaurant across the street from The Krusty Krab, a restaurant owned by Mr. Krabs.