Hey, can anyone tell me what's going on? The initial chaps were a mess. Who's the villain?...

for now, it's safe to say that the green guy is the villain. He was the villain in both season 1 and 2. The main characters are all the children who were once classmates, it changes pov per season on whose child. Season 1 pertains to jin, Season 2 to both kimoto and tehir, and Season 3 will be Garon. I think the plot will come to full circle once Jin recovered his memories. He seems to know a lot and acts very much different pre-amnesia.