After the news cuts and the episodes seem to be over, we're shown Marie, Jordan, Andre, and Emma all in a new state-of-the-art prison that is supposed to be a new version of the woods. Obviously, Cate and Sam were not the heroes that day, but to Homelander anyone trying to release more Supes into the world is a hero. There is a clear line in the sand drawn between pro-supes and anti-supes characters now and that will be the great divide of The Boys.
Our final shot shows Billy Butcher (Karl Urban) discovering the remnants of the woods. We also know that Neuman has an airborne disease that can kill supes, a chess piece she will likely use over Homelander once she is in office. The only person who knows Neuman is a supe however is Marie, who is in the underground prison as of now. It is not clear how evil Neuman is or what her motive exactly is, but she likely will yield the most power come season 4 of The Boys.
After all the deaths of humans at Godolkin and Homelander set to hit trial for his murder, I'm guessing that there will be some sort of punishment for Homelander. This will only lead to a bigger divide between Supes and humans, leading to an all-out war.