A street preacher in Detroit will mention bad things to come that are "grey and deadly", and a mention of 12 kings. The Grey Death was a pandemic in the original game, and the organization that was fought against was Majestic 12.
The game begins with a look at a statue, followed by Bob Page engaging in conspiratorial conversation.
An e-book in an apartment predicts the rise of nano-augmentation in roughly thirty years. (HR is set in 2027, the original was set in 2052.) In the convention center, advertisements can be seen regarding the development of nanoaugmentation.
A secession group called the New Sons of Freedom, or the NSF.
In the original Deus Ex, NSF stood for National Secessionist Front.
It had already been through one name change and kept the initials.
It is possible for your pilot to die in the game.
There is a character in both the original and HR who will be under attack, and will tell you to save yourself. You can listen to them, and they'll end up dying, or you can stay behind to save their life.
An NPC will question your decision on wearing sunglasses out at night.
Joseph Manderley is responsible for covering up key evidence from the Sarif attack and the Milwaukee incident.
Versalife is a manufacturer of the drug neuropozyne. They're also stated to be working on nanotechnology for medicinal purposes.
Page Industries is mentioned.
One of the researchers at Omega Ranch says in an email that he's started naming the babies they're genetically modifying to accept nano-augmentation after the apostles... Paul?
Several emails written by people with cyberlimbs, including powerful, well-educated people, are riddled with typos (much like Gunther's similarly misspelled emails from the first game) , the implication being a lack of feedback, or simple inexperience with augmented limbs, when it comes to finer tasks such as typing.
FEMA is being used for shady activities.
When Marik takes off from the Detroit factory the camera movement is identical to how Jock's helicopter takes off.
A tidbit of news seen on the TV will mention the sales of orange and lemon-lime soda.
A security guard at Tai Yong Medical will mention how another guard joked about getting the wrong soda from a vending machine.
A few notes from the Sarif Office theme in the prologue mission is from the UNATCO music. Example here (Starts around 2:20.)
There is mention of "Germans" working on a Skull-gun and gun enthusiasts' magazine carries an article titled "Skull Guns and Other Implanted Weaponry".
A newspaper article mentions plans to create a special UN branch to combat growing international terrorism.
The keycode for David Sarif's private elevator is 0451, which was also the keycode for the UNATCO storage shed, and continues the tradition it inherited from the System Shock duology of (0)451 being the first numerical keycode you have to enter in the game.
The area surrounding the hero's workplace starts out under attack, with hostages involved.
For the first real mission, the hero is asked which weapon he would prefer, each weapon supporting a different playstyle.
People are smuggling things out of the hero's workplace.
The first large area is a city in the USA with a very run-down slum that Adam has to go through, complete with big sewers and a lot of diseased bums. The enemies in this area put explosives at strategic points and have people on rooftops. There is a storage area that can be broken into, and a secret underground government base nearby.
And one of the gun smugglers you can find in the area is black and wearing a hoodie and sunglasses. The rescue of someone leads to him giving a discount.
The second large area is a city off the coast of China, where the protagonist must go to a nightclub and contact someone with ties to The Triads and the Tongs, as well as investigate a specific floor of a penthouse. The hero must also infiltrate a bio-corporation and comes into conflict with a Dragon Lady.
In this Chinese city, there is an optional conversation about the corruption of Western governments.
At some point, you will visit a major city where many people speak French. This French-speaking city is where the hero starts to really converse with AI.
A detective will greet you with a "in the flesh."
In Montreal you visit a secret underground lair that contains both the Illuminati logo on a hallway as well as a statue of the MJ-12 logo.
Morgan Everett is the CEO of Picus TV and Elizabeth DuClare is a spokeswoman for the World Health Organization.
Two of the achievements are named "Cloak & Daggers" and "Smash the State," the first of which was a passphrase and the latter of which was an NSF password.
Tong's son is seen boarding a ship named "The Tracer," and his intention is to go to Hong Kong. It's Tracer Tong.
Adam also gives Tong Junior a bit of advice that he promises to remember. It's a paraphrase of a line in the first game.
The "Taggert's Message" ending shows Adam walking into an office with a man who looks a lot like Joseph Manderley, suggesting he becomes the first UNATCO agent.
The biochip is a clear precursor to the mech-aug killphrases and the nano-aug killswitches
The basis of the conspiracy is to give people an affliction so that they will become dependent on a product which the conspiracy conveniently provides.
When Taggart and Sarif give their requests to Jensen on what to broadcast, just before leaving them, Jensen simply says, "I'll think about it," just like JC would 25 years later in Area 51.
A subtle one, there is an area in Hengsha that closely resembles the canal area in Wan Chai, even down to two police men standing off to one side, one warning the player that tourists better watch out away from the main areas, and the other not speaking English. Possibly not intended.
One of the items in the news ticker mentions a film named Invisible War shattering box office records.
"The Missing Link" features a young Gary Savage involved with the Hyron Project.
Scoring a hoop on a basketball court in a rough area of town earns the player some secret congratulations.
A Dr. Jankowski works in the LIMB clinic in Detroit.
An unseen worker on Panchea is named JC.
At the end of the game, talking to Taggart will have him mention that supporting him will eventually lead to a reorganized UN that would be able to combat issues such as terrorism. This could be a possible hint that Taggart's ending is the canon one.
A subtle moment in Montreal has you walking up to a globe being held by a hand, with the corridor and room you enter into being quite reminiscent of the room originally seen in the introduction to Deus Ex.
Executive Meddling: The reason why The Missing Link was DLC added later (rather than part of the core game, as originally intended) is because the game was rushed after being delayed repeatedly. This is the same explanation for the why the Tyrant boss battles are more "head-on" than series fans would've liked, since they were farmed out to third-party developers to save time during production (Which is also why two hub areas- Montreal and Upper Hengsha- were abandonced).
Fortunately, the Director's Cut puts everything back together (while maintaining the "separate but integral" feel of The Missing Link), and redesigns the boss battles to provide a much wider variety of options for dealing with them. Except the Hyron battle, which is completely unchanged.
There were originally going to be more city hubs in the game: Upper Heng Sha (which was even partially completed), Montreal (the devlopers' home city, which they were rather regretful for not managing to include) and even India. They didn't complete these due to lack of development time, not wanting to stretch out the story too much and so that they could focus on making fewer but bigger hubs.
They also stated that the lack of development time was the reason why the game's ending is literally chosen via button presses as opposed to something more involved. The endings themselves however, were exactly what they intended.
YMMV on that: the middle three at least would fit in quite well.
A conversation boss fight with Megan Reed, that would have revealed more about their failed relationship.
An alternate opening, that had you breaking into Sarif HQ as to test their security system. The fact that you were breaking into Sarif and not a competitor firm wouldn't be revealed until the end of the sequence.
You were originally supposed to be able to spare Fedorova and Namir after defeating them.
A cut level would have had you visit a Humanity Front rehabilitation clinic in Utah where people would have their augmentations removed. The rehab clinic would have secretly been home to a Purity First cell and was originally going to be where you had the social boss battle with Isaias Sandoval. The clinic was cut for time, but most of the completed content was moved to Detroit.
The Director's Cut reveals that Malik was originally intended to be Arabic and use Arabic swear words- while her VA could pronounce them right, the developers weren't happy and decided to change Malik into an American.
The Ty Yong Medical building was originally supposed to be arranged as a vertical factory, with a long shaft following the entire building and robotic production lines following the entire height of the building.