Fucked Up beyond All Recognition. Generally used in the context of a situation/operation/mission that is messed up so bad it is beyond salvaging. FUBAR comes after ATFU. Also generally used when describing something that is akin to a Monkey Shit Fight.
When I started working for this company, I just figured their M.O. was SNAFU, however, after a few months, I realized they were just ATFU, now given their current state, they are FUBAR.