Will try to summarise series 1 for those who missed it - if you intend to watch it then please beware there are spoilers …..
Series 1
Starts within Arnott leading a counter terrorist unit who mistakenly shoot an unarmed man when they enter the wrong flat number (he was wearing a baby carrier which the gunman mistakes at a split second glance for a bomb harness.)
Arnott was told by his superior officer than everyone in the raid should lie and say the man was displaying threatening behaviour so they had no choice but to shoot however Arnott refuses and is transferred to anti corruption unit AC-12.
The AC-12 team is the same as in series 2 - Hastings in charge with Arnott and Kate Fleming in his team.
AC12 are investigating Tony Gates who seems to have a unusually high crime conviction rate which they suspect he and his team are falsifying. Gates team includes Cotton (who's just turned up in series 2) and Bob the builder, Neil Morrissey.
During most of series 1 Kate is undercover in Tony Gates team.
Throughout series 1 Gates and his team are investigating drug dealing on a local estate. Three of the drug dealers are killed, two of which occur after Cotton leaves a stake out 15 minutes early. This is a hint that Cotton may be a bit dodgy although he claims in interview with AC12 that Gates gave him the order to leave early.
Married Gates is actually trying to conceal that he is having an affair with his childhood sweetheart, Jackie Laverty. He covers up a hit and run accident she caused resulting in the death of a man.
Gates later discovers that the man she 'accidentally' killed was in fact her accountant who had threatened to expose her money laundering activities for the drug trade. Gates decides to turn her in but she convinces him otherwise.
Jackie is murdered shortly afterwards under the orders of Tommy, the man behind the drug dealing on the estate and for whom she is laundering money (also the chap in witness protection, series 2.) Tommy frames Gates by putting his fingerprints on the murder weapon and then freezing Jackie's body and the weapon. Tommy uses this to blackmail Gates to carry on concealing his drug dealing on the estate and subsequent laundering of the money through Jackie's businesses.
Blackmailed by Tommy, Gates convinces his superiors that the drug dealing wasn't the issue for the three deaths on the estate and that it was a terrorist cell making bombs. Even though the evidence seems a bit flimsy to say the least (a chemistry book and a few household chemicals found in the house!) He police superiors seem keen to accept this alternative explanation for the deaths.
Whilst Gates is looking for the frozen body of Jackie, he comes across Arnott being tortured by Tommy and his gang and saves him. As a result
Arnott is convinced Gates is not all bad and together with AC12 they track Tommy by his phone to a local golf club.
Gates seizes Tommy and drives off from the golf course with him. Tommy confesses to the drug dealing, laundering and orders of his men to kill Jackie and the three drug dealers on the estate. Gates is wired and Tommy's confession is taped.
Hastings, Arnott and Kate from AC12 are following close behind them. Gates leaves Tommy handcuffed in the car, hands Arnott the taped confession and throws himself under a passing car so that he is killed in the line of duty and his police pension is still received by his wife and children.
In the meantime Cotton (who is now working alongside AC12 in series 2) has been promoted to take over from Gates. When questioned by a superior why he joined the police force he reveals that he was a young tearaway but after caddying for a man on the golf course he was encouraged to join the police force by him (Tommy.)
Our suspicion that Cotton is actually under the control of Tommy comes at the end when just after Tommy's arrest, Cotton asks for a quick word with Tommy under the guise of questioning. Cotton tips Tommy off that his best defence is to claim that the drug gang on the estate was actually
a terrorist cell making drugs. Tommy smiles and presumably he ended up in witness protection for testifying this fact.
It's a bit garbled and there's probably a lot of detail missing but that's the gist of series 1.