Gotham going From Bad to Worse ever since Batman left isn't entirely a coincidence. Remember, The Penguin was mayor for a time, and Word of God has confirmed that Commissioner Gordon is retired in this continuity. With a notorious super-criminal who executed people via firing squads being left in charge of the most crime-ridden city on Earth, it's no wonder everyone's having such a hard time keeping things together.
Most of Gotham's super-criminals from Riddler to Poison Ivy are staying awfully quiet in Arkham, despite the fact that a city without Batman would be ripe for the taking. Why aren't they out there causing trouble as per usual? Because without Batman, crime has no punchline.
Despite (supposedly) being dead, the Joker still continues to drive the chaos in Gotham, being responsible for the crux of the plot of Season 2 involving Kate's disappearance and the drive to find the painting that he himself made. This wouldn't be the first time he did thisbeyond the grave...
Also, he was responsible for the crux of the pre-series plot of Beth's disappearance and kidnapping on the Kane sisters' 13th birthday, meaning he's Connected All Along to the respective disappearance of a Kane woman.
Black Mask's comics counterpart ran his company's business into the ground, lacking the savvy to operate such a prestigious enterprise. Yet Gotham always had one company running around that proved to be impossible to compete with: Wayne Enterprises. Here, while it's clear that Black Mask is a little bit more business savvy, Wayne Enterprises isn't in the best of shape to take care of Gotham, especially considering that both Bruce Wayne and Kate Kane are gone, so even if most of his enterprise is being funded by drug money, he doesn't have a Fiction 500 company making it impossible to do business in Gotham.
August Cartwright's villainous actions and having been a colleague of one Dr. Jonathan Crane aren't entirely a coincidence. Cartwright had a very stressful relationship with his mother, yet was desperate to do anything he could to try and help her out. With Crane being an expert in phobias, he no doubt picked up on Cartwright's fears of both his mother's wrath and his fear of being unable to please her. It's not clear how long the two worked together, but at some point during their tenure, Crane could have whispered a few things in Cartwright's ear on exactly what to do, and Crane being a sociopath, it's not hard to guess what such suggestions entailed.
The bad batch of Snakebite causing people to become cannibals isn't unsurprising. The entirety of the substance is made, in part, with Scarecrow's fear toxin, which is supposed to show people their worst fears. Now, fear happens to be a byproduct of our natural instinct to survive, making us scared to do anything that could possibly put our life in danger. One of those natural instincts is to eat, out of fear of starvation (and thus dying). Take the fear toxin and mess up the Snakebite in the worst possible way, and it brings out the person's most basic instinct up to eleven.
Crossed over with Fridge Horror; the same episode also proves Heath Ledger's Joker correct. "When the chips are down, these... civilized people? They'll eat each other." He wasn't a monster; he's just ahead of the curve.
Additionally, in reference to the same film, Lucius Fox designed the new Batsuit to be more agile, with him joking about it being effective against cat bites (seeing as Bruce specifically asked him if it would be effective against dogs). Ryan is able to handle the bites of the infected without issue, since her suit is strong enough to withstand them (seeing as only Kryptonite can pierce the suit).
When Ryan first learns that Alice loves Ocean during their team-up, she relents on her a little and is more willing to help her save him along with Angelique... only to change her mind and handcuff her to a fence once Alice taunts her about how her relationship with Angelique won't last due to the latter's criminal tendencies. It isn't just a case of Alice pissing her off — Ryan realizes that Alice is right! Hence the part where she lets Angelique go when the latter asks Ryan to leave Gotham behind with her, choosing to help change Gotham instead. Not only that, Ryan probably realizes that Alice, the woman who indirectly caused the death of the mother, has more of a chance at a relationship with Ocean than the former does with Angelique and finds that really unfair. This is why she tells Alice that she will save Ocean from her; why should Alice, a mass murderer, get love when Ryan is struggling? It may also put her reaction to Ocean's death and Alice's apology in a new context.
Alice suffers delusions in season 3 reflecting her secret desires, fears, and guilt. She eventually deduces it's because she's no longer in control of her life and Mary claims it's the cumulation of all the suffering Alice inflicted. This makes more sense when one recalls that in the previous season, Enigma made Alice and Ocean regain their memories of their time together in Coryana, so Alice's emerging conscience was also restored.
Throughout the first season, and especially in the last two episodes of season 1, "A Secret Kept From All The Rest" and "O, Mouse!", we see The Crows, Jacob in particular, act as an antagonistic Inspector Javert towards Batwoman due to distrusting vigilantes. This is a trope seen time and time again in fiction, and is most likely quite reminiscent of Quentin Lance's distrust of The Hood/The Arrow in the first few seasons of Arrow. Except, when you really think about it, there's a key difference: The Crows aren't the police, even if they constantly act like they are. They are a private security firm, and as stated in "O, Mouse!", Batwoman's work is done for free. Thus, there's a good chance that Jacob's real reason for disliking Batwoman is because she helps people for free, thus effectively muscling in on their Punch-Clock Hero business system, and acting as a rival to them. While public officials like Quentin Lance and other typical examples of the Inspector Javert archetype have valid reasons for hating vigilantes that align with their personal moral code, Jacob may well just be motivated by profit.
Similarly, while Catherine Hamilton's death is genuinely horrific, one does have to wonder why her company was developing a neurotoxin deliberately designed to kill slowly and painfully (without even bothering to synthesize a cure), especially when the use of chemical and biological agents of this kind is considered a war crime in any armed conflict, raising the question of who, exactly, Hamilton Dynamics was intending to sell it to.
Mabel Cartwright's domineering attitude and abuse of Alice out of jealousy over her beauty cast a darker light on August being a Mad Doctor specializing in skin graft masks. His experiments were likely not just to help his son, but his mother, meaning that Mabel's obsession with her vanity screwed up the next two generations of her family.
Plus, as much as August was dominated by her, he clearly got his entitlement, Control Freak tendencies, and manipulative parenting from somewhere...
This also makes his enabling Mabel's treatment of Alice much more unsettling. Perhaps as long as someone else is his mother's punching bag, then he doesn't have to be.
The revelation that Enigma is indeed Riddler's daughter spells trouble for poor Ocean if the Prince of Puzzles ever finds out his own flesh and blood was killed by his hands, especially if he decides to follow in his Arkham counterpart's footsteps. Fortunately for Ocean, his death means Riddler can't get his hands on him. Alice, on the other hand... better hope Riddler's in a different cell block in Arkham.
There may be a chance that Black Mask not only knows Kate is Batwoman, but he now knows that Bruce Wayne is Batman.
Black Mask is in Arkham. However, there isn't any sign of the corrupt GCPD officers being arrested along with him. They could still be at large.
