Golden Abyss is set shortly before Uncharted: Drake's Fortune, and follows Nate as he helps Marissa Chase, a young woman determined to continue her dying grandfather's research. Along the way Nate finds himself clashing with his former friend, Jason Dante, who is out to steal the research for his own means, along with the formidable warlord Roberto Guerro who wants to use the treasure to fund his conflict.
This game provides examples of:
- Big Bad Duumvirate: Roberto Guerro and Jason Dante.
- Black-and-White Morality: From the very beginning, it is clear that Dante is only doing this for the money and doesn't care of anyone but himself. Even after discovering that the gold is irradiated, he still plans to sell them to the black market, not caring of what would happen to any potential victims.
- Body Horror: The protagonists discover the remains of the Quivirans beneath the ancient city and upon closer inspection, they find out their bodies are deformed. At first they suspect it might be a birth defect of some kind but it turns out that the Quivirans died from radiation poisoning.
- Call-Forward: Like in Drake's Fortune, Sully interrupts Nate and Chase as they are about to kiss.
- Continuity Nod:
- Dante brings up Nate obsessing over Francis Drake's ring.
- Nate once again brings up his fear of clowns when Chase asks him if he was raised in a circus.
- Gilligan Cut: Drake is told to "go crying back to Sully," which prompts him to snap back with, "I don't need Sully". Immediately followed by "Sully, I need you!" in the next scene.
- Jump Scare: In Chapter 31 on Crushing mode, the body of Esteban will suddenly comes to life, scaring Chase. This is an outtake made during the motion capture of the game. Through a series of chuckles Chase's actor scolds the game developers for scaring her and accuses Nate and Esteban's actors for being part of the prank.
- The Load: Chase is not as helpful as Elena or any of Nate's allies. Not only does she fail to decipher any of game's clues, she also spends most of the time being captured by the bad guys. She's also pretty much useless in combat, apparently having a fear of guns. It isn't until the final few chapters that she decides to carry her own weight and help out.
- Press X to Not Die: The two only bosses of the game require players to swipe the screen according to the correct prompt.
- Redshirt Army: Apparently because of lack of funding, proper equipment and training, Guerro's men are considerably weaker compared to Dante's mercenaries.
- Roaring Rampage of Revenge: Angered over Guerro abandoning him and attempting to get the treasure before him, Dante vows revenge and hires a group of mercenaries to take on Guerro's army.
- Running Gag: Dante complaining his turtle shoes getting dirty.
- Saved by Canon: No matter what trouble Drake and Sully get into, they'll survive the events of the game so they can appear in the canonically later main series games.
- Spin-Off: The first portable game in the series.
- Story Breadcrumbs: This is one of the biggest things different about Golden Abyss. All of the hidden collectibles have some connection to the plot; most of them are pieces of evidence you collect while searching around, like a GPS surveying tool that has bullet holes in it. Even the turquoise rocks you find have a glyph on them with some Kuna mythology details.
- Title Drop: Drake says the game's title in Chapter 31 after he and Chase found the Lost City of Gold, the same named Friar Marcos wrote in his letters.