Just three seasons into Gotham, and already Gotham City has gone from the lovely hometown Thomas and Martha Wayne took good care of to the crime-infested terror that will soon prompt their son to dress up as a bat in his spare time. By the May 1 episode, Bruce Wayne is training to be the hero that the city needs; Jim Gordon and Harvey Bullock are effectively running the GCPD; and several villains from the comics have emerged and started plaguing the city. For instance, the Court of Owls' secret weapon, which they plan to use to reform the city in their image, is the type of storyline that would be right at home in a much more established Batman storyline than the prequel Gotham was originally meant to be.
The Court have decided that they need to destroy Gotham City in order to take control. And with a unanimous vote, including Jim's uncle Frank Gordon, the Court of Owls decide that they will authorize the use of a "weapon" that will wipe out most of the population in order to remove the undesirable crime element. (Of course, it seems, that the Court also caused it by funding human experimentation; torturing Arkham patients; and discovering a scientific way to literally resurrect people.) Anyway, they've already taken Bruce Wayne out of the equation by sending him away to what seems like a remote mountain location. Though, until he actually gets outside, I'm skeptical that he's really left Gotham.
The nature of the weapon still hasn't been revealed yet, but Gotham does give out some clues. When Barbara and Tabitha go down to the docks to check it out, they discover that the weapon was delivered in a box labeled "Indian Hill," which means that some part of the experiments designed and run by Hugo Strange is responsible for it. Here's a guess: maybe it's Alice Tetch's blood — which was last seen before the season's super-long hiatus — and was nearly weaponized multiple times, including a close call with the Court Of Owls, before Jim was able to stop Jervis Tetch. And it's been established several times throughout the show that when people die, they end up getting sent to Indian Hill, if the sinister Strange wanted to take a look.
Whatever the nature of this weapon, it arrives in a pretty small box. So in future episodes, it will be interesting to see what reasonably-sized item could possibly be used to totally destroy Gotham City on the whim of the ever-sinister Court of Owls.