Haseo's initial revenge story gains more layers as he meets the various characters throughout the game and interacts with them both through cutscenes and with the game's MMO-like social tools. There's a mail feature that offers ways for Haseo to interact with party members outside of battle, such as with characters sharing rumors of tidbits they read about online. There are also marriage events where Haseo can marry certain characters after showing enough interest in them. Getting to learn more about the characters this way is an intriguing addition to the game, mirroring the many different ways you might interact with people in real life.

The .hack// series is renowned for its plot that pits the player inside of an MMORPG called The World, going after nefarious foes who kill other player avatars, causing terrible side effects for the real people controlling them. Last Recode tells the revenge story of Haseo who hunts these player killers within The World, as well as how he grows along the way from a cold, uncaring warrior into a much more reliable protagonist over time. The added fourth volume also goes a long way to build upon the established plot within the MMO and its characters, concluding the story on a strong note that feels complete.

The hack-and-slash gameplay of the overworld combat evolves over time, with only a handful of abilities available at the start, with many more opening up organically as the game progresses. Haseo gains access to different weapon types over time, like dual blades, broadswords and scythes. He also learns many abilities that give him a degree of control over his enemies, where the correct timing with button presses allows him to stop an opponent's attack altogether.

In battle, as Haseo and his party deal special attacks, a gauge fills up over time, giving the option for powerful, flashy Awakening attacks that decimate the enemies on the field. These attacks can be used to quickly deal damage in a pinch or finish off a group of foes.