This episode was great! It brought all of the plot together finally so we can actually see what season 2 is about. I don't get how a bunch of you haven't clued in....
By now it's clear that the premise of season 2 is based on the virus and an alternate strain of the virus that, if everything happens like Peter sees in the future, would wipe out almost all of mankind.
The paintings HRG saw was the vaccine that Bob asked Mohinder to give (which would be the first major cause besides Hiro of all the disaster to come), him shooting the guy (which he already did), HRG himself dying, Nicki doing something, and I forget the other. All of these paintings, like Isaac's previous paintings from season 1, lead to the upcoming disaster like a puzzle.
The root cause of all this is really Hiro. Hiro has turned Kensei over into a man cut so deep that he will never heal from emotion. He is the one ravaging through season 2 killing off some of the heroes.
The next puzzle piece is Bob and the vaccine. I believe Niki has been given the vaccine already, which is why she is now able to work with Mohinder and why she is in the painting. It is in her that the vaccine will mutate and spread.
Next is Takeizo Kensei himself. He is now taking down the older heroes one by one. It is him that the whole symbol comes from - if you remember, this was his flag in the past. He has changed his name to Adam, and it is possible that he is even Peter's father.
Peter was at Kensei/Adam's house before he teleported to the future using Hiro's power which he absorbed in season 1. In the future, Peter will likely encounter an insane takeizo kensei, but maybe not. I'm not sure what he will discover in the future.
Next is West and Claire. Slowly, Claire is being turned against her father and is starting to stand up for herself. I think that a crucial moment will be when the time comes for HRG's death painting will take place. If he dies, West and Claire become the new bad guys. If he avoids it, we will see....
Matt and Nathan are essential for bringing the Heroes together again. They will help draw the trail first to the 'Boogeyman' and then with the heroes united against the boogeyman, they will be able to, if they cooperate with each other, stop the virus from spreading and stop Kensei.
From there..... I'm not quite sure....
Anyways, that's my theory and I'm sticking to it.

