- Nathan climbs across the hands of a giant clock tower, in an homage to Safety Last!.
- One of the missions is titled The Brothers Drake.
- The action of the Drake brothers giving each other a boost to reach a broken ladder with the second brother sending a way across is one for Brothers: A Tale of Two Sons.
- Earlier in the game, there's an Age Cut scene from young Nathan to the older Nathan, who subsequently gets punched in the face, just like Indy in Indiana Jones and the Last Crusade.
- The young, blond founder of Libertalia who has a monkey as his pirate sigil and Sam "doesn't recognize" is a reference to Guybrush Threepwood, the protagonist of classic pirate adventure game Monkey Island. If you look at his burnt painting in King's Bay, you can even see the first two letters of his name are "Gu", Sam speculates he rose to become a fearsome swordsman, and later Nate will mention "That's the second-biggest cistern I've ever seen" in his tower.note
- In the epilogue, you can find and inspect a copy of The Nameless City by Faith Erin Hicks. This is an actual recent release; the artist previously worked on a comic for The Last of Us.
- Also in the epilogue, in Cassie's room you can find a poster for Savage Starlight 2. Savage Starlight was the comic series that Joel and Ellie kept collecting in The Last of Us.
- You can have Nate and Sully visit a busy passport office in Chapter 11. Sully remarks how dreadful it will be having to deal with long lines to get back to the States. Nate replies that it will be nowhere near as bad as entering Arstotzka.
- At one point, Nathan plays the original Crash Bandicoot on a PS1. The real kicker? It's a fully emulated level that you're required to play during the cutscene.
- The old lady Evelyn is British, used to be a prolific and famous archaeologist, lives alone in a mansion filled with relics, explored Xi'an, China in her youth, ties back her hair, and has a gun and knows how to use it. If not for the name, Evelyn would be a dead ringer for an elderly Lara Croft.
- During the flashback at Evelyn's mansion, Nate and Sam find a book written by T.E. Lawrence, which prompts Sam to remark that he always wanted to see Lawrence of Arabia. This also doubles as a Continuity Nod to Uncharted 3, which involved Nate retracing one of Lawrence's adventures in Arabia.
- Nate's stage name during his magic phase was "Nate the Great", the name of a children's book series.
- Considering the subject matter, it's unsurprising to see a number of visual nods to The Goonies toward the end, including pirate skeletons (who died in similar circumstances) around a long dinner table, and a pirate ship intact inside a large cavern.
- After reading one of the old letters regarding the pirate civil war in Libertalia, Nate compares the situation to Lord of the Flies.
Shout Out / Uncharted 4: A Thief's End