Warning! Spoilers ahead for Batman Beyond: Neo-Year #5
Gotham City has changed a lot in the decades which set up the Batman Beyond era, but the city has one surprising weakness that is shared both by the future version of Bruce Wayne's city and the one seen in Christopher Nolan's Dark Knight trilogy.
Terry McGinnis is facing what may be his most difficult foe ever, and he's doing it without the help of his deceased mentor, Bruce Wayne. Technology has caused Gotham City itself to become sentient, and therefore pleased with its stagnant level of crime. Never one to be content, Batman is continuing his fight against criminality (and Gotham's wishes), leading the city to activate a new warrior dubbed 'the Sword of Gotham' to relentlessly attack Batman wherever he appears.
In Batman Beyond: Neo-Year #5 by Collin Kelly, Jackson Lanzing, and Max Dunbar, the new Terry McGinnis is forced to deal with the fact that 'the Sword of Gotham' are actually citizens of the city itself, who have had their minds twisted into violent agents of Gotham due to nanotechnology quietly implanted into their bodies. But how could a malevolent intelligence infect everyday people with a device meant to transform them into deadly threats? The answer is familiar, and once again highlights the critical weakness in Gotham's infrastructure: Gotham put the nanotechnology into the city's water supply instead.
It's kind of strange that the water supply is still a vulnerability in Gotham's infrastructure in the future considering how many times it's been exploited in the past. On several occasions, Joker has used the water supply to disperse his toxin throughout the city. Also, as seen in Batman Begins, Scarecrow used the water supply as a delivery mechanism for his fear gas. One would think that after so many villains have broken into the water supply in the past, Gotham would finally up the security.
Then again, in this storyline it is Gotham itself that is doing the exploiting. So it makes sense from a logistical standpoint. If anyone would know how best to manipulate the citizens of Gotham it would be the living embodiment of this city itself. Gotham would know its own weaknesses and vulnerabilities and if it were to try and infect its own population in the most efficient way possible then of course it would use the same means as villains have in the past. But still, it's quite bizarre that even in Batman Beyond's time all these years later that same weakness is still around.