The first one is definitely a classic and has a lot of interesting discussions of ideologies and transmunanist philosophies.
The conspiracy theory plot in the original year 2000 Deus Ex is really well-written and researched, to the point that if you didn't know it was created much earlier you'd think was based on 9/11 conspiracy theories and/or Covid-19 conspiracy theories. So unlike many things, this thing really ages well due to the writing being top-notch and perennially relevant.
for people who don't mind being spoiled:
In Deus Ex, you're part of a future "war on terror" special ops unit that was created after a terrorist attack on a NYC landmark - the statue of liberty. There's a global pandemic, and you discover that you are part of a deep state / shadow organization that is behind that and was behind the original terrorist attack as a false-flag operation, and is using the vaccine for the plague to control people. There are an Antifa type organization too, fighting against the entrenched powers. And all this written before 9/11 even happened.
Another game that delivers the same sort of musing would be Bioshock, although Bioshock is musing about what would happen if you implemented Ayn Rand's objectivism ideology of capitalism in its extremity. The Deus Ex future is more plausible than this one however, which is frankly more a fantastical what-if, unless you think that the government is going to collapse and big pharma will take over, and literally everyone will morph into mutant homicidal dope fiends, ruled over, in the rubble, by a cyber-mutant Jeff Bezos.
Both games came out of the same original place however, the remnants of Looking Glass Studios. So it's not really a surprise that they're similar. The lead designer for Deus Ex was the original creator for System Shock, while the lead designer for Bioshock made System Shock 2.