Became a sort of vigilante after the first night, went looking for the Others.
He is actually working for Widmore and was put on the plane to serve as a scout in preparation for the freighter team. This would explain his secretive nature and why Goodwin called him a "bad person".
This theory is supported by Ben's statement that the people on the freighter (who worked for Widmore) were "the bad guys" and Goodwin said that Nathan was "not a good person". Not a good person=bad guy
He has Crohn’s disease, ulcerative colitis or another digestive disorder.
This would explain why he would have spent the entire flight in the bathroom and why his bathroom trips in the jungle were so lengthy.
He was doing something inappropriate in the jungle that they wouldn't want the show's child audience to hear for two hours ...
He was part of a different faction, not an Other and not a follower of Jacob but perhaps a follower of the Man in Black?
During his "trips" he was following a vision of some kind.
It's well known that every other reference to Canada or being Canadian in Lost, is indicative of deception. It stands to reason that Nathan may not actually be Canadian at all, or if he is (which would mean he is the only true Canadian in the entire series), then he was being deceptive in some other way.
Leading theories include the above mentioned connection to Widmore.
Equally likely (perhaps even moreso) is that Nathan was indeed an 'Other'. This does not mean he wasn't on the plane (there is little evidence either way) - adding credibility to him potentially being Widmore's victim, or the person who was holding the camera. His long disappearance may be the result of him meeting one of the Others secretly to give them the video tape (that was later shown to Locke by Ben).
This does not explain however why he was referred to as a bad person by both Goodwin and Ben. One theory is that (while previously living amongst the Others), he took a liking to Juliet. As Goodwin was having an affair with her at the time, and Ben's affections for Juliet well known, their individual jealousy could have led them to believing he was 'bad'. Another reasonable theory is that Nathan somehow conspired with Widmore in some way. If he was Widmore's victim, he may have divulged information to him that he was not supposed to (perhaps under duress/torture).
Nathan is not seen at all during the crash/rescue scenes. We first see him exactly 10 minutes into the episode 'The Other 48 Days', right next to Ana Lucia and seconds before several Others are heard nearby waking up the survivors as Eko kills two of them (triggering his 40 days of silence). This is not to say that Nathan appeared to the survivors for the first time at that point - but the fact WE see all the others in the initial crash scenes except Nathan seems a deliberate tactic on the part of the writers.
Watch carefully at the looks that Goodwin and Nathan give each other thoughout the episode. Some of the looks could be interpreted as some sort of familiarity with each other - which over time turns into looks of frustration. Was Nathan purposely deflecting attention from Goodwin so he would not be caught out by an increasingly paranoid Ana Lucia?
He does not seem to sound Canadian. When first put in the hole by Ana Lucia, he yells 'let me out' several times. There's absolutely no evidence of accent at all! (Canadians have a very distinctive way of pronouncing the word 'out').