I am convinced that there is at least one unknown temporal operative in Heroes.
Most of my convincing is a result of late last season. In Five Years Gone, Hiro encountered an unpleasant future. Between that episode and How to Stop an Exploding Man, no other established characters went to the future. Hiro himself had contact only with Ando, Kaito, Sylar, and Nathan. It is almost certain that this contact with Nathan was what convinced Nathan to fly Peter out. However, it is unlikely that any of the other contacts were of significant effect.
According to Five Years Gone, Sylar, HRG, Nathan, DL, Niki, Molly, Mohinder, and Candace had survived, presumably by not being in the area when the explosion happened. Had Nathan not flown Peter away, all of them except possibly Nathan would have died in the explosion. Additionally, Hana and possibly Linderman were implied to be alive. Linderman, canonically, was killed by DL, which could potentially have been avoided by moving up the timeframe of the explosion (which would, itself, have probably killed him). Hana's death, on the other hand, was part of a mostly separate sequence of events, with no obvious outside influences.
It is highly unlikely that Hiro's influence would have changed all this. I submit, then, my theory: At least one other time-traveler, probably in company with someone with the power of emotional manipulation (like the Haitian's father, whose name I can never remember), was working more-or-less independently of Hiro, although it seems likely that he or she knew what Hiro was doing so they wouldn't interfere with each other. Alternate!Future!Hiro is a possibility, although the Future!Hiro we've seen probably isn't. This individual's goals are not something I care to speculate on at this time.