Monster Train 2 is a strategy game in which players control an alliance of angels and demons aboard a train to battle the Titans who have invaded Heaven. The game features five distinct clans, each offering unique gameplay mechanics and strategies across three levels of vertical defense. Players build their decks through unit recruitment, card upgrades, and a new room and equipment card system that provides strategic advantages and unit upgrades. The game’s hub, the Covenant Outpost, serves as the central location for story progression.

TRON Catalyst casts the player as an Exo, a courier program living and working in the capital of the Arc Network. A mysterious package detonates, fundamentally changing the courier's purpose and granting him an unauthorized power called the Glitch. This ability gives him the ability to see and manipulate system time loops that periodically reset the environment. The Guardians of Order immediately begin chasing the hero to take control of this new ability, and the protagonist must confront Conn, a separate sinister program with its own agenda.