The season finale isn't far away, and one big plan may wrap up most of Gotham Season 3's many storylines. The Court of Owls is using the Alice Tetch virus in order to exterminate the people in the city that the Court finds unsavory and unappealing. But it's surprising when Captain Barnes returns to Gotham... and his single mission is to kill Jim Gordon. Now, Jim is pretty guilty when it comes to colluding with criminals in order to get his way, considering that he secretly joined the Court while deceiving the cops and pretending that his uncle died in a completely unrelated situation. In fact, at this point it would probably be better for Jim to warn as many people as he can about the Court's plan before Captain Barnes, still deep in the throes of his infection (but still alive, despite months of incubation), tracks Jim down.
Here's what makes me curious, though: I understand how Kathryn discovered Jim, because he's foiled their plans many times, but what purpose did Jim, at any point, serve for the Court? Kathryn told Frank that she wanted him to join because he could help their plans go more smoothly, but he was never really all that helpful. It doesn't seem that the Court really needs anyone from the police department in order to do their bidding, and Jim never really investigated anything beyond delivering the Riddler to the Court's prison. Speaking of, now that Jim has led both Riddler and Penguin to the Court's prison, I hope those two are able to work it out and become friends again.
So when Barnes track Jim down, I suppose there's a few things that could happen. Of course, Barnes could kill or infect Jim... that's probably unlikely, given that he's the main character of the show. It's probably more likely that Barnes could help Lucius Fox put together a cure for the virus, possibly dying in the process. And it will be interesting to see how Lee, who is onto Jim's deception, reacts to the Court's plan. She's incredibly cynical now — maybe she'll be convinced to join the Court if it means getting rid of people like Jim.
I'm guessing that the city won't be destroyed by the virus, but it's possible that it could go off in some area — maybe it will even be turned against the Court in an ironic twist, making them lose their inhibitions and tear one another limb from limb in a twist on how their leader sees the rest of Gotham as uncivilized and criminal.