yeay there's only 2 timelines. the 3rd timeline is the happy ending that is created when u beat the game.
in T1, Missile dies, goes to the junkyard, meets Sissel, Sissel does his(her?) own thing, Missle does his own thing, then goes back to Yomiel's death, then chills for 10 years to start the events of the game that I guess we can call T2.
Missile does have the power to rewind time. Remember Kamila dies and he goes back to save her, killing the Park Ranger instead. We do get to see Kamila die, and it's also foreshadowed earlier when Sissel notices she has a core when he sees her kidnapped.
this brings 2 questions to my mind;
since Missile can rewind time, why didnt he just rewind it to before he talked to Sissel and convinced him to help right there instead of waiting 10 years?? Lynne was already dead when he met Sissel so he coulda easily done that. Of course, if he did that, then we wouldnt have a premise for the game =P
question 2 is during T1, why was Yomiel present when he went to Lynne's house? He should have still had his body knocked over and snatched away by the fake doctor and pigeon man / Cabanela.