The second half of Season Three would be about some renegade members of the League of Assassins, led by a man named Kobra. Kobra is actually the twin brother of Jason Burr, the scientist from Season One? That's a fundamental part of his backstory in the comics, so we have to keep it here. Kobra is Jason Burr's twin, and he was raised within a cult in India. He eventually learned that his twin brother was killed by the League, so he chose to infiltrate it Nd try to take it down from the inside. Both as revenge for his sibling (who he barely knew) and as a way to increase the power of his own cult. He'd end up coming to Gotham with Whisper A'Daire and Kyle Abbot after the League implodes, and he starts trying to export his cult into America via Gotham City.
This half of the season would also feature OMAC and Brother Eye, who I plan to pretty much portray as rip-offs of Doctor Who's Cybermen. They already kind of are that, I just want to fully solidify that. Brother Eye was created by the Council who created all those clones of Paul Kirk in Season One. Paul managed to destroy the Council, but Brother Eye had already gained his sentience by then. Now he's formed an alliance with Kobra. An alliance that leads to mass genetic experimentation as Brother Eye keeps creating new OMAC units. Considering the indiscriminate way in which Brother Eye targets people, pretty much everyone in Gotham ends up opposed to it (including most of the city's criminals).
You may be wondering: Is Paul Kirk dead? I…I don't know. I don't really have strong feelings one way or the other. But I know that his one episode of Beware the Batman never got any good follow up, and I was accidentally reminded of OMAC when I went looking Google for ideas for a season two of Beware the Batman. Apparently people did have some ideas online, but I don't think any escalated to the level of the stuff I'm writing here. But that reminded me of OMAC and Brother Eye, so here we are.
Oh, and I do want to revisit Poison Ivy, Bane and Mr. Freeze. Since the League basically imploded, these three ended up back in Gotham for good. This time, they're now temporarily allies of Batman and the Outsiders. Why? Well, it's simple. OMAC is fundamentally robotic, and these three are at least a two thirds majority association of eco-terrorists. In fact, I think we need to add Professor Pyg and Mister Toad to this alliance. They're weird eco-terrorists too, and I can only imagine they wouldn't be treated too kindly by the robotic legions swarming Gotham. And Cypher (the weird robotic man with mind control powers from Beware the Batman season 1) would be an important member of Kobra and Brother Eye's legions. He fits too well with this storylines robotics theme, and he also never get enough attention way back in season one.
So season three ends with this storyline involving Kobra and Brother Eye as the main antagonists. The season would end in a suitably dramatic fashion, too. I see Gotham being ravaged by the OMAC program. Hell, the whole globe was probably really messed up by that one. So after this incredibly deadly situation is finally dealt with, I can only see a timeskip being the best way to end the season and begin a fourth one. Because I do have some plans for a fourth season. The fourth season would just be way shorter than seasons one through three (around 13 episodes instead of 26) and it'd mostly exist to help wrap up Anarky's storyline.