I googled it during one of the ad breaks - Morse and Thursday had rumbled corruption in the higher echelons of the local police force. There was a shoot-out at the end of the last series -
From Wikipedia....."In the final episode, the looming merger of city and county police and misgivings about corruption, lead Thursday to consider retirement, in response to strong hints from C.S. Bright about age and health. Disheartened by this, Morse speculates to Monica about leaving the police and going abroad with her. Assistant Chief Constable Clive Deare asks Thursday and Morse to covertly investigate corruption within the police and council. Morse is sent to a rendezvous where he is ambushed by corrupt officers and Thursday is lured to Blenheim Vale, a derelict former wayward boys home, where there was rampant sexual and physical abuse (of which Jakes was a victim). Morse escapes the ambush and goes to support Thursday, who is shot by Deare, a participant in the abuse at Blenheim Vale. Deare tells Morse he has framed him for the murder of Chief Constable Rupert Standish. Deare is about to kill Morse when he is shot dead by a girl who had also been abused at Blenheim Vale, who then kills herself. Bright and Strange show up with backup and an ambulance. As Thursday is being loaded into an ambulance, Morse is arrested by officers from another force for the murder of Chief Constable Standish. The series ends with Thursday's fate unknown and Morse in a jail cell."
At the very beginning of yesterday's first episode there was a voice over saying that an enquiry had exonerated Morse, but that he was still temporarily suspended from duty. Half way through the chief of police was saying that it would be good to have Morse back - and it then seemed that the choice was down to Morse himself - which was a bit weird. Mind you, plotwise I think that was the least of my problems!