In his recent article, Adonis Gonzalez put forward a pretty sweet theory, that in fact the Joker WE know hasn't been born yet, but will be the product of the unholy union between Barbara Keen and Jerome Velaska.
It's a strong theory, however there is one thing that actually, in light of not only recent events but the ramped up graphic nature of the show this season that would seriously work instead.
I agree that we will see Barbara and Jerome become a proto-version of Joker/Harley during this season, but something very controversial may happen and it's all linked to Morena Baccarin and Ben McKenzie hooking up in real life.
Fair warning, this is a very dark theory, so if you are squeamish or hate spoilers... might not want to read on!
At some point, we know there will be a "showdown" of sorts between Lee & Barbara & Jerome but it won't be what you think.
Barbara makes clear to Jerome she wants Lee to suffer but not for the obvious reason. It's because Gordon has finally gotten across to her that she did not kill her parents, and that he still loves her destroying her fantasy. She is hoping that by targeting Lee, Jim will rescue her and kill Jerome.
Jerome takes this the wrong way and in a home invasion scenario RAPES Lee while Jim is incapacitated!
The horror of the act snaps Barbara back into her "normal" self and she tries to prevent it, leading to her death from a head injury and Jerome escaping.
Lee's horror at what has happened leads her to clear up any evidence of the rape (as the medical examiner she could do this) and the police assume that she and Barbara struggled when Barbara attacked her, which she doesn't refute.
Months pass and it becomes clear Lee is pregnant (as Morena is in real life) with Jerome's child. She is forced to pretend the child is Jim's, all the time being taunted by Jerome from afar.
Lee is distant during the pregnancy and Gordon is so busy dealing with the Maniax that he misses scans etc, causing rifts in their relationship. Lee is horrified at what is going on but can't tell the truth and Jim's putting the case over her gives her at least the chance to buy time.
Of all people it is Edward Nygma who begins to work out the "riddle" as he notices things and while he didn't examine Lee, he saw some things were missed - seemingly on purpose. He and Miss Kringle are now together (from him saving her in the GPD massacre) but his arrogant inner/alter ego now believes he can also have Lee as well via some blackmail, after all if she "let" Jerome and Jim have her, why not him right?
As the season builds to its finale and Lee is about 8 months pregnant, Nygma makes his move and is rebuffed. He is seen by Miss Kringle in the process and in his first public rage knocks Lee flying.
She goes into labor however there are complications and Lee is in serious danger.
"Good" Nygma reveals his understanding of what happened the night of Barbara's death and his own battle with a demon inside him to Gordon, and that Lee has also had this for months, knowing she is giving birth to future Maniax.
Gordon puts this to Lee and she reveals the truth, that she is carrying Jerome's TWINS!
A boy and a girl, she gives birth and quickly whispers something to Gordon which distresses him even more than the news of the rape, he gets a rage look on his face, grabs his gun and leaves, Lee then passes away in his absence.
Meanwhile Bullock spots Jerome entering the hospital, just before Lee is due to give birth. After all, he couldn't resist watching for himself. Bullock is shot and Jerome wounded, which draws Jim. Jerome escapes without knowing of the twins birth, only that Lee died, and taunts Jim with this.
Jim is prepared to murder Jerome but Bullock, wounded and dying steps in front, preventing the shot as "there's too much at stake for this". Jerome fires another round anyway and runs away laughing as it hits Harvey.
Jim tells him what Lee had whispered, that Barbara died saving her and he's not losing him too!
Bullock in his last moments tells Jim that like it or not he is a father now, and he has to get the boy as far away from Gotham as possible if he's ever gonna have a chance. If Jerome finds him or he learns about his past then he'd be the devil himself.
Bullock's last words are that he always wanted a daughter, and that he always liked the name Barbara. Whatever he decides don't let the boy be called Harvey, you can't trust any of 'em (a little nod to the future Two-Face) and he dies in Jim's arms.
A devastated Gordon walks back and is handed the baby girl, as they believe he is the father. While the boy is in an incubator and Lee's body lies recently deceased.
He decides raise Barbara as his own daughter, through connections with Falcone he sends the boy away, swearing Nygma to life-secrecy in exchange for just losing his job rather than going to Arkham. He swears he will kill Nygma if it ever gets out.
The season ends with Jim returning to Barbara's apartment (which she left to him) with his new daughter, and the boy being taken to a family by Don Falcone.
Nygma returns to his apartment a broken man, having lost his job and Miss Kringle having moved all her belongings out. He smashes a mirror and writes a large question mark in blood on the wall. Jerome, still wounded comes into view of a very big house... Wayne Manor, where at the start of season 3 we see how far Bruce's training has come when Jerome pays a visit.
This would also fit in more with the Bruce and Jim dynamic for a season 3, with Bruce being almost a brother for baby Barbara at times and show as she gets older, the reason for the trust he puts in her.
Years in the future, Barbara becomes BatGirl, while her unknown brother might come across someold Maniax videos from Gotham or be sent some riddles as to who his father is, he gets to Gotham, dons a red hood... and the rest is history!
This also allows for Jerome to STILL be The older, Hamil style Joker, and the boy to be brought up under a different name, Jason Todd for example?
What if Joker always KNEW what he was doing in both crippling BatGirl and killing Robin? A Death In The Family suddenly has a whole new meaning!
This is an extreme theory for sure, and one that may be controversial on TV. Where those events would lead with the canon we know and love are mind blowing in themselves, it is clear from the second episode of the season that this show is going much darker this time out. While this kills off several major characters in one go, this would likely be the moment the "gruff" Jim Gordon is born, a man who lost it all except the daughter that isn't even his. Who views this as his penance for killing a man, the man who builds a bat signal when the time comes.
From the casting perspective, Morena Baccarin is not likely to be part of season 3. Between being a new mother and starring in the Deadpool movie, she's gonna be too busy.
Bullock has always been set for a heroic death, protecting the secret of the babies would be a very noble way for him to go and bittersweet as he himself was finally settling down.
Barbara will have run her course as a character, the idea of her and Jim settling down is not possible with what they've built, but that she dies the person he loved rather than the crazy she thought she was gives her a good resolution.
It also allows season three to progress as it needs to as some of the younger actors will inevitably age as Bruce is clearly starting to, maybe even skipping a year or two. If for any reason the show wasn't picked up... it'd also serve as a jaw dropping finale, setting up much of the future canon we know and love. Hell, next time we see Jerome after Bruce sees him off might be in a court room, being prosecuted by one Harvey Dent setting up another villain.
While the TV company may have some reservations about using rape in such a context, it would only serve to make Jerome more of a monster and if done properly "offscreen", say focused on a shot of Barbara's dead body then the rest can be implied. It may court controversy, but it would put Gotham into that "must see TV" bracket for sure and symbolise the beginning of "The Rape Of Gotham" by the criminals, that culminates in Batman.