I should probably preface this with my own estimate of Atton's age. Judging by the fact that he served in both wars, with a little guesswork, I estimate him to be between 30 - 32 years old at the start of Kotor II. I could draw up a little timeline, but again, this is pure guesswork on my part. For reference, at the start of the game the Exile is estimated in his/her mid-30's (around 35-36) and Revan, around 40.
The Mandalorian War
There is absolutely nothing revealed about Atton's family or childhood in any of the dialogue. The first point we arrive at in his history is that he joined the Republic forces at some point during the Mandalorian war. He refers to Revan as having "saved them", and probably served under Revan's command. It's my guess that he was a pilot of some kind, probably a fighter pilot.
As far as who he knew during the war, it's pretty obvious that he did not serve with the Exile, or if he did, he was of a low enough rank that they would not have met in person; he and Bao-Dur didn't seem to recognize one another either. Atton was possibly at the battle of Malachor V; this didn't make it into the final version of the game, and is only revealed in one of the removed wav files. If so, then we can assume Atton barely escaped the gravity well caused by the Mass-Shadow Generator along with the other survivors of the battle.
The Jedi Civil War
The Jedi Civil War began not long after the destruction of Malachor V. Much like Admiral Saul Karath from KotOR I, when Revan turned on the Republic, Atton followed and became a Sith soldier. It is obvious he did it out of loyalty. Whatever had happened out there on the battlefields during the war, Revan had earned his respect and admiration. As I speculated before, he believed that Revan saved him and his comrades, while the Jedi Council did nothing to aid the Republic.
Once with Revan's Sith forces, Atton was singled out for special training, because of his (then unknown) Force sensitivity. It's implied that Revan had many Force sensitives trained to become hunters and assassins of Jedi, Atton among them. Their natural affinity with the Force allowed them to escape the notice of Jedi, to sneak up on them and hide thoughts and intentions from them. It's unclear exactly how many Jedi Atton really killed, but the number is probably somewhere in the hundreds.
One day, a Jedi woman sought him out. She seemed to know about him, about what he was and what Revan was doing, how Revan was corrupting and using other Force users and breaking their will. This Jedi was able to break through Atton's mental defenses and open his mind to the Force, proving to him that he was indeed a Force Sensitive. He killed her - in fact, he implies that she died willingly, to keep his secret hidden - but her words and actions left him open to the Force. Atton fled to Nar Shaddaa and changed his name (implied - this may also have happened later) in an attempt to leave the Sith.
From here, his history gets a little fuzzy again. It's unclear, for example, at what point he changed his name, or even how many times he changed it. We can guess that he probably did some odd jobs on Nar Shaddaa and other worlds - smuggling, blockade running, and so on - for various criminal organizations, until he wound up in jail on Peragus station and met the Exile. Why he was in jail on Peragus is also open to debate. I have two possible theories about this. One - the one I think is more likely - is that he was the illegal weapons courier who was smuggling contraband in to the miners (you find some of it in the dormitory). My other theory is that he was sent by the Exchange to pick up the Exile from Coorta & co., although that puts a decidedly sinister tint on his motives for helping the Exile get off of Peragus.
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