When Deeks is later arrested, the team learn Deeks supposedly murdered his former partner, Francis Boyle back when he was a rookie detective and work to clear his name. ... Eventually, Kensi fully recovers and resumes her place on the team and her partnership with Deeks.

What episode does Deeks tell Kensi he killed Boyle?

In Cancel Christmas, Deeks comes clean to Kensi and confesses that he did kill Boyle, to protect Tiffany.

Who did Marty Deeks kill?

He didn't get along with his former partner

On "Internal Affairs" (Season 7, Episode 7), we finally found out Deeks was being investigated for the murder of his former partner, Francis Boyle.