[Mild SPOILERS for the Gotham season 2 finale ahead.]
Gotham will finish its season 2 descent into madness with the finale episode tonight, titled 'Transference'. Whereas the first half of Gotham's second season focused on Theo (James Frain) and Tabitha Galavan (Jessica Lucas), as well as the larger Order of St. Dumas' vengeance-fueled quest to kill Bruce Wayne (David Mazouz) and 'cleanse' Gotham, the second half of this season has revealed that there are more insidious forces in the eponymous city than secret religious orders seeking to settle centuries-old grudges. The mastermind behind the machinations of recent episodes has been that of Dr. Hugo Strange (BD Wong): the head honcho at Arkham Asylum, who has been resurrecting such villains as Fish Mooney (Jada Pinkett Smith) and Theo Galavan as the deadly Azrael in his spare time, via his Indian Hill facility.
However, even as Jim Gordan (Ben McKenzie) and young Bruce have uncovered Strange's connections to the many terrible things that have been happening in Gotham of late - not to mention, the death of Bruce's parents in season 1 - it has become clearer and clearer that the not-so-good doctor is but the tip of the iceberg. As teased in the 'Transference' promo (see above), Gotham season 2 will wrap up by revealing more about not only Strange's goals, but his superiors' too.
Gotham executive producer John Stephens was interviewed by CBR about the show's season 2 finale and offered some insight into how the events of 'Transference' set up plot threads for Gotham season 3 - specifically, when it comes to Strange's goals and those of his bosses, a.k.a. the Court of Owls:
We're going to understand [Hugo Strange's] endgame in the finale. We're going to understand that he received a directive from his employers, who gave him a very specific directive, specifically about reanimation. That is something which his employers, who we know are the Court of Owls, is going to be paid off in Season 3 when we understand why they wanted him to do this thing. We will understand in this season what exactly he was supposed to achieve, although part of that we will pay off next year, too. It plays into our overarcing Court of Owls' mythology.
Gotham's version of the Court of Owls should be significantly different than the organization's DC Comics counterpart. Showrunner Bruno Heller, along with his fellow writers/producers, has seemingly been planning to incorporate the group into the show's mythology since the very beginning of season 2. Stephens, for his part, told CBR that the Court of Owls are an Illuminati-style "shadowy group of powerful people" who have controlled Gotham City for centuries - and may, in fact, be the true masterminds behind the deaths of Bruce Wayne's parents. As to whom, exactly, the Court of Owls is interested in reanimating, that remains a mystery, though whoever it is the Court wants them to have their memories intact too. That's why Fish's return from the dead with her memory in season 2 is such a big deal, according to Stephens:
[That's] incredibly important. That is the key. That is what we will discover Hugo Strange has been up to all this time, is to resurrect somebody who has their full personality. That is what the key members of the Court of Owls want him to achieve.
Of course, Strange's experiments have also attracted too much attention to remain in the shadows any longer and Stephens confirmed to CBR that what's been going on at Indian Hill (as well as Arkham Asylum) will affect Gotham City as a whole, when the show examines the fallout from the events of 'Transference' in season 3:
The Pandora's Box gets opened at the end of the [season 2 finale] in a way that is going to have a huge effect in the entire city. The city we return to in Season 3 will be very different than the city we leave at the end of Season 2.
That means even more super-villains will be roaming the streets of Gotham City in season 3 - and Stephens even confirmed some of the baddies that will be showing up on Gotham next season to CBR:
"We'll be seeing Mad Hatter in Season 3. We'll be seeing the Tweedle Brothers, too, if we're going to bring the Hatter in. In line with the Court of Owls, we'll be seeing Talon. And, we should be seeing Solomon Grundy."
Mad Hatter a.k.a. Dr. Jervis Tetch was originally supposed to appear on Gotham season 2, but given everything else that's been happening on the show of late (see the story threads featuring the Order of St. Dumas, Mr. Freeze, Hugo Strange, Clayface, and so on), it's not surprising that he ended up getting pushed back to season 3. The character, traditionally a scientist who uses mind-controlling technology on his victims, is known for dressing up in a manner that resembles the famous character of the same name from Alice in Wonderland. Similarly, the Tweedle Brothers (a.k.a. Dumfree and Deever Tweeds) are a pair of criminals who resemble Tweedledum and Tweedledee from Wonderland, and in the New 52 DC Comics universe they have been working with Mad Hatter - something that will presumably hold true on Gotham too, by the sound of it.
Meanwhile, the DC Comics zombie super-villain Solomon Grundy has previously appeared on such live-action DC TV shows as Smallville and Arrow (where he showed up in season 2) and some fans have speculated that we've glimpsed him lurking around in the background at Indian Hill on Gotham season 2. Last, but not least, Talon a.k.a. William Cobb is a deadly assassin employed by the Court of Owls - though outside of those who have read Greg Capullo and Scott Snyder's Court of Owls comic book storylines (Batman: The Court of Owls, Batman: Night of the Owls), odds are most Gotham fans and Batman fans in general won't be familiar with the particular character before he shows up on Gotham season 3.
Gotham season 2 concludes with 'Transference' tonight. Season 3 will air on FOX in fall 2016.