When Batman confronts the Psychiatrist, He gets killed by Ra's Al Ghul who was Hugo Strange's master. When Strange is about to die, he activates Protocol 11 which destroys the office of Wonder Tower, thus forcing Batman to flee the building with Ra's. After Batman lands, we can hear and witness in the game itself that there are still TYGER forces in the game, particularly the helicopters.
TYGER Command Center: All air units report in, Cease attack and return to base immediately. Repeat, return to base immediately.
So what happened to the TYGER guards, particularly those who are in the helicopter?
Follow-up question: Why didn't they attack Batman afterwards, considering that the Dark Knight is their target? Most likely they find out that Batman killed their Boss, Hugo Strange, but they didn't know the truth that Ra's Al Ghul killed Hugo Strange.
Best Answer
Most of the Guards had post-hypnotic suggestion, and it is implied that every Tyger Guard was either a hypnotized inmate or a mercenary who was mentally hypnotized to do strange's bidding. When Strange Died, they were like a chicken with its head cut off; they had no idea what to do, so they simply returned to base and awaited further order, however the GCPD came into Arkham city and rounded up the Tyger Guards and began dismantling Arkham City. In short, they had no more instructions, so returned to base/Arkham Island (if you unlocked that story) and sat around until GCPD regained control. In game, the helicopters de-spawn (to head back to base in theory).