There are six jobs available at launch, including the Reapers, a class which can shoot twice if the previous shot defeats an enemy, and the Boomers, a demolition expert specializing in the use of explosives.

The game is the last in the series chronologically, and, as with SteamWorld Heist, takes place after the destruction of Earth by a runaway fusion reaction at the end of Dig 2.

Set a couple decades after the events of Steamworld Heist, the story begins in the tranquil area of Caribbea as pirate captain Quincy Leeway recovers his submarine from the Royal Navy, the ruling faction of Dieselbots that controls the Shard, with the help of two close comrades, Daisy Clutch and Wesley Hotchkiss.

Leeway's crew has been stealing the ill-gotten gains of the Navy, who are oppressing the Steambots due to an ongoing water contamination crisis that has resulted in a "disease" called Rust.

However, he is haunted by an inferiority complex due to the exploits of his mother, Krakenbane, a legendary monster hunter who left him the submarine, while he has accomplished little.

Leeway's crew faces off against Morgan, the leader of the cult, and slays her, stealing the naval ram from her flagship and using it to enter the ice cap to the north.

In an act of sadistic spitte, Leeway gets marooned on a desert island instead of killed to try to break his spirit and force him to see the Kraken destroy everything he holds dear.

Leeway proceeds to free the captured crew, and also discovers that Piper Faraday, protagonist of SteamWorld Heist, and her crewmate Fen, have been secretly helping him all along.

He recovers enough fuel rods to augment his ship's boiler, allowing it to dive to the deep ocean and, with Faraday's guidance, find a group of peaceful Atomics.

The remaining Atomics come up to the surface to live alongside Steambots, some reformed Navy members help rebuild the damage caused by the Kraken and Piper and Fen leave with Krakenbane to space to fight evil.

[11] Dan Stapleton wrote that SteamWorld Heist II "takes place on a surprisingly large overworld map that’s packed with so many tough and tactically deep turn-based missions", and added that the experience took him about 40 hours to finish.

[4] In a more negative review, Katharine Castle from Eurogamer wrote that the core gameplay was still "eminently enjoyable", though its bigger scope and ambition meant that player progression became too slow and missions in late game "feel progressively less like a fun, cheeky outing to steal some treasure, and more like an openly hostile grind where you barely escape with your life".