John Neil is an agent with British Intelligence.
It is likely that it is Military Intelligence that Neil works for. He had been for quite a few years, more than he would like to remember, been a highly respected and often used member of the prestigious and elite Special Air Squadron (SAS) and there is a definitely mention that he was being recalled to service by the Regiment (as that branch is often called). Still, whether it is they or whether they are just acting as talent brokers is not certain. The work that he will be asked to take part in is definitely deep undercover, not the sort of thing he would have been doing for the SAS, more like what MI6 or Special Branch or some other undesignated group might requite.
The initial operation for which he is called back into action is in Northern Ireland, taking place some time after the Accords had supposedly brought an end to the far too long running conflict between the Crown and the notorious IRA and its numerous splinter groups; word had reached the shadowy world of Intelligence that there was a rabid sect determined to undermine the Accords and force both sides into renewed warfare in the hope of uniting all those still angry with the ceasefire. Once that lengthy mission was finally brought to an end, the usefulness of Neil was too evident to let him walk way into obscurity - there was always something else to challenge him with.
When we meet him, Neil is a dead man, of sorts, in two different ways. The first, more obvious, way is the fact that he is going undercover taking the role of a man who had left Northern Ireland many, many years before. That man had died but the news of his departure was kept quiet to allow Neil to take his place in a return to that region. The second way, though, was not so apparent and it came from the fact that Neil was a man who was for the most part dead inside.
Everything Neil had loved and worked for and fully expected to live with for years to come had been taken from him in a terrorist explosion. His much loved wife, his son, and the unborn child she was carrying were killed horribly and Neil was close enough to hear the screams but not near enough to save them or, as he secretly wished, pass away with them.
After those horrible events, he had been sent 'home' in exile in his beloved Highlands to recover, as if that could ever happen, and to await a call by Randall, his primary controller in the Regiment, to come back to work. As we meet him a year has passed since that summons, a series of months where he was put through multiple batteries of tests, some physical and many psychological, to see if he was ready for duty. We are told: "a year later, gaunt and empty, dried of all tears, he'd been ready to go back, needed to get back into action". Interestingly, "the psychologists didn't agree" but they were not the ones making the decisions.