His change is largely adrenaline based, after his 'combat' is complete he is able to take stock of his emotions and his feelings about killing a man.
His eyes are described as containing 'the cold gleam of the fanatic' - he is assured of what he is doing. He is a young man, a student, but he has seen death before. He is avid, hungry to shoot when he sees the armoured car, only the practicalities of getting through its shell stops him.
Eventually, he kills a solider and an old woman, and later when he is planning his escape 'His hand trembled with eagerness' to kill the other sniper. However, he is caught in a situation of kill or be killed. He must be a fanatic to survive because he faces another sniper who is just as fanatical.
It is only when the other man is dead can he allow himself to feel remorse and curse the war. He realises that the other sniper is very like him in almost every way except that he was a free stater and the titular sniper is a Republican. The reality of death is what effects him the most.
There is a long tradition inIrelandof armed rebellion and an equally long mythos which presents this as honourable and glorious. The war between the free staters and Republicans was termed the war of brothers fighting brothers or the Cogadh na gCarad or “War of the Friends” - “it is a curious fact that the Irish Civil War of 1922-23 often found brothers fighting on opposite sides” (Boyce 106) Both sides obviously believed they were in the 'right' so to speak.
As such the sniper is torn between this belief in the honour and moral right of his combat but the realisation that in order to win he must kill his 'brother.' Not his literal brother, but rather his fellow Irishmen. Flaherty does leave it ambiguous as to whether the man is a figurative brother or his actual brother, since the man may well have been his brother in arms before the army split in 1921, perhaps it is his real brother, or perhaps it is the recognition that this man, like him in so many ways, could be his brother because they are so similar.