The 1st one. It has all the real conspiracy stuff.

The others are effectively soft-reboots.

Deus Ex, the original, was made pre-2000 yet it has some features 1st person shooters to this day fail to include in the game.

Once you get over the graphics, control scheme, and old animations, you will be constantly impressed by the game to a degree where you're embarrassed for modern developers. You'll be constantly asking "How does this game have this feature in 2000!?" and "I can do that!?"

• Melee headshots that can insta-knockout depending on what angle you hit the head (back of head with blunt weapon means unconscious, not kill).
• Individual health bars for each body part, applicable for enemies as well as the main character.
• Getting shot in both legs forces you to crawl, basically the Fallout VATS system.
• Pacifist playthrough possible.
• Corner peeking/leaning with Q and E.
• Fully voice acted.
• RPG character building with leveling system based on discovery not combat.
• Movable bodies that can be detected by enemies.
• Stealth with respect to lighting system/shadows and footsteps.
• Weapon upgrade kits to customize your favorite weapons.
• Jumping puzzles with alternate paths based on skills chosen and movable boxes you have to stack to get places.
• RPG side quests that significantly change how you approach the map (passkeys, clues to broken doors, contacts that give you things)
• NPC branching dialogue options.
• Hack robots from terminals to do your bidding.
• Augmentations that act like magic spells; invisibility, night vision, increased jumping, super strength, shields, regeneration, etc...
• Passcodes DON'T require you to get them to use. Which means, as long as you remember all passcodes from your previous playthrough, you are effectively psychic. Good for speedruns.
• Shooting, dropping or throwing items grabs enemys' attention.
• You can set traps for enemies with mines and drop boxes on them (very rigid box physics mind you).
• You can get a kit to control the Missile Launcher's missile with your crosshair.
• Attache inventory system like Resident Evil.
• Magazine based ammo system, not bullet based. Which means if you have 8/9 bullets with 3 magazines and reload, you lose those 8 bullets and your magazines go down to 2. This is intentional to balance item usage and deemphasize run and gun. Plus, more realistic. Not for everyone, though.
• There's a noisy cricket 1shot gun called the PS20 as a get-out-of-jail-free tool. Good for bosses your build is bad against.
• You can eavesdrop on enemies who talk to one another and they will sometimes reveal secrets about the map.

Now, looking at all that, remember... This game came out in 2000, along side MGS and Zelda: Majora's Mask. That was a good year for games, aye?

Remember, the original Deus Ex is far ahead of its time in so many ways, it's almost prophetic. Take a break after playing it, because many similar games will only let you down on how much Deus Ex actually has over them.

Start with this one, then move to Human Revolution, skipping Invisible War.

Or, play Deus Ex: Invisible War at your leisure. It is a red-headed step child and tries to be what other games were when it came out, not succeed the original. In other words, it cuts a lot of the original game's best features in order to appeal to console-oriented gamers. Story is fine, but going to it straight from Deus Ex is like a kick in the nutsack.

Human Revolution is a great run of the mill cover shooter with a few of these nice mechanics fleshed out a bit, but doesn't expound on anything too much.

Mankind Divided should be the next after that, but I never got far into it because it streamlined a lot of the RPG adventure/sandbox elements for a Dishonored type of run-gun stealth shooter.