When Sheldon and Leonard head over to Penny's apartment to drop off a package that arrived for her, Sheldon is bothered by how messy her apartment is.  Later that night, Sheldon sneaks into Penny's apartment to clean and organize it.  Leonard catches him and tries to stop him, but Sheldon is obsessed.  Penny wakes up and yells at them, Leonard asked how she knew.  Apparently Sheldon left an organizational diagram in her closet.  Sheldon goes to apologize, but Penny doesn't believe him.  When Leonard goes to apologize, Penny accepts and hugs him.