
"Puzzle Agent 2 takes the low-key weirdness of the original in fittingly strange new directions, but the puzzles themselves lack bite and variety."

Nelson Tethers (Character) returns as an agent of the obscure "Department of Puzzle Research" branch of the FBI. After solving his case in the first game, Tethers isn't satisfied with the result of his investigation. Isaac Davner, the foreman of the eraser factory, is still missing and the Hidden People (Character) are still a source of mystery in the town of Scoggins, Minnesota. The FBI's Department of Puzzle Research considers the case closed, but Nelson isn't sure why. Why does the FBI seem to not care? Desperate to solve the remaining mysteries, Nelson decides to go rogue and head back to Scoggins to try to finish what he started. While this particular storyline ends in Puzzle Agent 2, the end does hint at the possibility of a Puzzle Agent game set in Bermuda, presumably with a new story.
Similar to the first game (and other recent puzzle-based story games such as Professor Layton (Franchise)), Puzzle Agent 2 focuses on following a narrative while searching for clues and solving puzzles as they are presented to the player. Puzzles can be of many types, and hints will be available to players who become stuck. Each puzzle has 3 hints, which become more revealing as the player uses more of them.
Graham Annable (Person), designer of the first game, has said that the team is paying attention to feedback from the first game and working at making the sequel as good as possible. The gameplay is quoted as being "similar, but better". Annable has also said that now they have the chance to expand the story and include more of the arc.
