I was making a big write up of my season 4 ideas but it kinda became too big and the end was a huge info dump that didn't really make sense so I'm gonna condense it to bullet points for your reading (dis)pleasure. Also worth noting that this is what I would have liked to see in a potential season 4 that's realistic-ish. Ideally, I would make this a Batwoman show, but that wouldn't happen in reality, so this is still the Batman Jr. show we already had.
This is gonna go character by character (no particular order, just what feels right to me).
-Marquis is extremely remorseful of his criminal past and tries to better himself by going to a former-villain support group
-This support group includes Magpie, the S3 Mad Hatter, Wolf Spider, an older flamboyant man who wears pink, and Beth Kane.
-Nobody else knows Beth is back, only Marquis. They end up becoming close; they're an endgame couple in my mind. It's a good way to keep them both in the fold.
-Marquis mostly takes responsibility for his crimes, but also blames his mother, making them distant. He uses some of his fortune to fund Mary's clinic, no strings attached.
-Beth couldn't keep away from Gotham and moonlights as a vigilante. She keeps trying and failing to keep her "Alice side" under wraps.
-The Bat Team has no idea she's in town or being a vigilante, and she doesn't want them to.
-Whole season she's trying to be just Beth and push Alice away. By the end, she decides to reach a middle ground.
-She's attacked by an assassin who would kill her if Luke didn't save her just in time. The assassin gets away. She accidentally namedrops Luke and just decides to reveal herself to him
-They work together to find the assassin (more on that later)
-Mary's clinic is better than ever thanks to Marquis's help, and she makes more of an effort to work there than on the Bat Team
-Throughout the season, she gets closer to Luke. They don't become official here, but it becomes clearer than ever that they'll be a thing
-This one is just a spitball idea, but I'm thinking she keeps hearing a voice in her head, telling her to use more herbal remedies and natural medicines on her patients. By the end of the season, this is revealed to be a sporeling left behind by Poison Ivy, and she ends up becoming her own character, separating from her host.
-Luke is becoming a more independent hero, still working with Ryan, of course, but making strides all his own.
-He now has his first nemesis: Lady Vic, the assassin that attacked Beth.
-He keeps Beth being back in town a secret, and works with her to take Vic down
-Sophie and Ryan have been dating for a few months at this point, but the honeymoon phase is over, and things aren't going too smoothly.
-Sophie keeps arranging for time alone with Ryan, only for her to be stood up or Ryan changing plans last minute for family or Bat duties
-Between that and Sophie starting to feel like she's not pulling her weight on the Bat Team, she's feeling dissatisfied.
-By the end, she breaks up with Ryan (on good terms) and also decides to start being her own hero. After a talk with Mary, she gets the inspiration to become Hawkfire; she begins operating alone. Not permanently, just until she can be sure she doesn't *need* Ryan.
(I feel a little bad because I think constantly jumping partners is a gay/lesbian stereotype, but I just frankly don't want those two together)
-Ryan is making strides in relationship with both her mother and brother. After the turmoil of season 3, she wants them more in her life.
-She keeps overhearing Jada talk secretively in hushed tones, but writes it off as private business phonecalls. Until she hears "Black Glove".
-Of course, while trying to bridge the gaps in her family, she's fighting the main villain of the season: Lord Death Man.
-Lord Death Man is pure chaos. His goals seem unclear, and he's seemingly trying to cause as much destruction as possible. And he's good at it.
-After it becomes clear that Batwoman will be a nuisance to him, he surprises the team by destroying the Bat Cave. Not just the one under Wayne Tower, but all of them.
-LDM is seemingly immortal, feels no pain, and is superhumanly strong, making him especially hard to take down despite not being as cunning or plotting as previous villains. He's also more comical.
-In the end, despite heavy destruction, Ryan takes down LDM, and she finds out who he is: Bruce Wayne. Despite the revelation, she doesn't know how Bruce ended up like this nor how to fix him, and she ends up having to contact Supergirl on a way to lock him up. (I have ideas for how he got that way, but that's a season 5 reveal. Also, you might be thinking "well since Bruce is found, Kate can come back". I think at this rate, though, it'd be better if she just didn't so I'd just make some other excuse as to why she's still gone)
-Lady Vic, as I came up with a few years back, is none other than Julia Pennyworth. After Dr. Rhyme, her memory is still all sorts of messed up, and her work in Europe eventually led her down the path of an assassin.
-She's hired to take down all the members of the Bat Team, and she starts with Beth, where Luke intervenes.
-By the end of the season, Luke and Beth take her down, and Luke is keen on sending her to Arkham or prison, but he needs to go help Ryan, so he leaves her with Beth.
-Beth sees herself in Julia. Or rather, she sees Alice in Julia. She decides that Julia is too far gone and can't be fixed, and kills her (this is hypicritical, which Beth know internally, but it's a split second decision that she fights with in the next season). This is Beth's beginning as Red Alice.
-Before killing her, Beth asks who hired Julia. She only responds with one word: "Hurt". (Beth passes this info onto the others)
-Jada has been trying to stay close with Ryan, but a wrench is thrown in when Ryan confronts her after hearing her mention the Black Glove.
-Jada spills. It turns out she's still working for the Black Glove Society, but now against her will. The previous group was a much smaller part of a large and centuries-old crime syndicate. The BGS know Ryan is Batwoman and is leveraging her life over Jada to get her to work for them.
-Ryan asks who leads the Black Glove, and Jada tells her simply, "Hurt".
-Ryan makes the connection and realizes that Hurt was already breaking the deal with Jada by sending Lady Vic after the Bat Team, and that Jada needs to get away from him.
-The season ends with Ryan going to Jada and finally asking her something she's been feeling. Is Bruce Wayne her father?
-Jada initially laughs at the question, but then she sees that Ryan is serious. She confirms that Bruce and her had a fling, but Bruce is not her father.
-Ryan pressures her into telling her who it is, then. Jada gives in and tells her, "It's Hurt. Your father is Simon Hurt."
Also had a couple of filler episode ideas.
-The flamboyant man in pink from Marquis and Beth's support group ends up defecting and becoming a criminal again. Turns out he was the Flamigo. Marquis, Beth, and Evan Blake (Wolf Spider) work together to stop him. The episode strengthens Beth and Marquis's relationship, and also shows that Evan has given up his criminal life for good.
-A return of Cluemaster episode. Stephanie Brown also comes back, and by the end of the episode, Luke and Stephanie decide that they can't pursue a relationship. But Stephanie pushes him to try and be with Mary.