Adaptational Villainy: Crystal Brown is apparently getting this, since she's apparently willing to sell out her daughter to her ex-husband, who had just tried to kill Stephanie, whereas in previous continuity she cared a lot for her daughter.
Defied with Bard, who Batman opts not to work with after he arranged for Penguin to find Carmine, which led to the death of several men. Batman doesn't kill or allow people to be killed.
Continuity Nod: Cross-continuity, that is. Upon the reveal of Blackfire as a major villain, the death of said villain in Batman The Cult is gone over by Vicki Vale's newspaper in summary for new readers.
There is mention of Nightwing's "Death" from Forever Evil when Batgirl talks to Red Hood.
Corrupt Politician: Mayor Hady is finally directly identified as one in Issue 2 by his "kingmaker" Carmine Falcone.
Dirty Cop: By the time of Batman #28, the nightly patrols of GCPD officers either beat you to a pulp for breaking curfew, or escort you to an illegal nightclub.
Invoked by Mayor Hady and Carmine Falcone when looking for a new Commissioner of Police. The man they choose is perfectly aware of who the latter is and what he wants, and has no hesitation in turning the police department into just another cog in The Roman/Carmine Falcone's war on masks.
Somewhat subverting the norm, when the Obviously Corrupt Forbes takes the reigns of Commissioner, most of the unnamed officers and SWAT unit appear to follow his example, but mostly due to Just Following Orders. When given the chance to defy him, they willingly support Jason Barb's Batman Gambit to force Forbes into charging Falcone's men, and expose himself as corrupt to give them the evidence to take him down.
Dirty Coward: Forbes again: when briefly kidnapped by one of Falcone's men to take him to Falcone, and when he gets there and Falcone is displeased with him, he is clearly terrified.
The Flash Forward at the end of the first issue implies this will somehow lead to Bruce Wayne, unmasked and with the bat-symbol carved into his chest, tied to a broken batsignal while Gotham burns. It's stated in Issue 3 that Cluemaster, Lock-up, and two other minor villains are working for someone who might be manipulating everyone, even possibly Falcone and Batman, to take over Gotham. In Issue 10, Falcone hints that someone else was behind him deciding to go back to Gotham.
Evil vs. Evil: The man behind Gordon's disgrace specifically mentions that he'll be targeting the Penguin as well as Batman. By issue #7 he's destroyed Penguin's casino and legacy.
The chronologically later Batman #28 implies that Catwoman, as the new leader of Gotham's underworld, has mutual enemies with Batman, inclining her towards being a Friendly Enemy in spite of her proclaimed withdrawal from the Villainesses Want Heroes trope.
Foregone Conclusion: Anyone who's read Batman #28 knows that Selina, not Carmine Falcone, will gain control of the Gotham underworld.
Foreshadowing: The new Kingpin of Gotham's casino is called the Egyptian. There's two giant statues of cats in the background. As shown in Batman #28, it's Catwoman.
He's Back: Carmine Falcone, and Deacon Blackfire return as villains. The former was killed by Two-face in previous continuity, and the latter had a single (though beloved) storyline back in the 1980's. The former is more of an example in-universe, however, since he's getting revenge for being taken out of power, while the latter is out-of-universe. Minor villains Cluemaster and Lock-up also return.
Hollywood Law: One-sided version regarding Gordon's trial. The trial itself is played fine, but the heroes' treatment of it implies that Gordon should be let off if it is proven that someone else drugged him or otherwise messed with him to cause the incident that allowed his imprisonment, ignoring that Gordon's actions caused, as Jack Forbes notes, "manslaughter on a massive scale". While attention is given to the idea that the track itself could have been sabotaged, there is still the fact that Gordon did pull the trigger, something he and the judge on the case are aware of, but the Batfamily and many members of the GCPD do not seem to acknowledge.
How We Got Here: The story opens on "The End", where Bruce is chained to a broken Bat-Signal with the bat-logo carved into his bare chest as the city burns around him and the presumed Big Bad taunts him.
Batman and Catwoman's reaction to Carmine Falcone's return.
Penguin when the above mentioned villain is revealed to be attacking him on all fronts before he's ready.
The cops loyal to Gordon experience this and some Heroic BSOD when Forbes is revealed as Commissioner. It's a bit less fear and more outright shock, since they realize exactly what this means for the department during the gang war.
Pineapple Surprise: Stephanie Brown does this to her father the Cluemaster in #3; pulling the pin on one of the smoke canisters hanging on his costume when he tries to shoot her.
Reasonable Authority Figure: Gordon is so much this in Issue 1 that even when he is arrested, he doesn't object at all, letting himself be held accountable for the law, and telling any who try to stop the arrest to let it be. To a degree, Falcone is one: he doesn't pull You Have Failed Me on his subordinates when he's mad at them, unlike Penguin...
Running Gag: Nobody gives Arthur Brown the respect to just call him Cluemaster.
Smug Smiler: Major Forbes is almost flagrantly corrupt and hostile towards both Commissioner Gordon and Batman, and when the former is arrested for the subway incident, he can't stop smirking and crowing over Gordon's misfortune and has this expression plastered on his face when declared Interim Commissioner.
Spanner in the Works: Stephanie Brown earns her moniker of Spoiler when she escapes her father's criminal conspiracy in issue #3. By the time of Batman #28, she's become the Living MacGuffin people are offering millions to obtain.
Harper Row to Red Robin. She not only hacks his computer, but she breaks into his hideout while he's in the middle of an investigation and sneaks onto his plane.
Bard manages to derail Carmine's plans, and get Forbes, him, and Penguin arrested.
Catwoman will become the new leader of the Gotham underworld here.
Harper Row will become a costumed hero named Bluebird.
Stephanie Brown will go from a normal girl to the Spoiler.
Took a Level in Jerkass: While certainly a bad father before the relaunch, The Cluemaster had his occasional Pet the Dog moments with his daughter and very rarely attempted to engage her in battle. Relaunch Cluemaster had no quarrel with pulling a gun on and attempting to kill his defenseless, pre-vigilante daughter.
Tyrant Takes the Helm: Jack Forbes becomes the interim commissioner of the GCPD, and immediately takes everyone off of every case, including stopping the brewing gang war and being on the lookout for various super villains, in order to make the entire force aimed at taking down Batman, regardless of how much they are needed elsewhere. He even let Professor Pyg go after Batman left him gift-wrapped to send a message that he doesn't work with Batman.
Unexpected Character: Various characters come into play to bring back old elements of the Batman mythos that haven't reappeared in a long time. Key examples are Blackfire, who was in one story in the '80s and never really came back barring one exception, and Julia Pennyworth, who has not been seen since the '80s either.
In Issue 9: "Subjet's name is Julia." "Julia Pennyworth".
Wham Shot: While the character's return had been announced earlier, fans wary of any Smallville comic hijinks were thrilled with the last page of Batman #28: Stephanie Brown in a Spoiler costume, as the Living MacGuffin Batman had assaulted the Egyptian to recover.
Preceding that was The Reveal of Selina Kyle as the new Kingpin of Gotham.
Whole Costume Reference: Bluebird's new costume (blue and black with domino mask and popped collar) resembles the Pre-New 52 aesthetic of Nightwing so much that fans initially thought she would inherit his codename.