The crew of the starship Swordfish are on a mission to engage with space pirates when their battle takes an unexpected turn. With their jump drive activated without a destination, they find themselves flung across the galaxy to the galactic core. The Swordfish is badly damaged, and only 26 of the crew survive, including six qualified for combat. They locate planet Farworld, which is under attack by relentless mechanical aliens dubbed "Berserkers". The crew must fight back against the Berserkers and explore the galaxy to find a way back home. Cyber Knight is an RPG set in a science-fiction theme of being lost in an alien galaxy. The game takes place in a top-down view for movement on planets and areas, a side-view for combat sequences, and a first person menu system when aboard the Swordfish starship. The crew can travel between stars, scanning worlds for information. When landing on a planet, three crew members piloting three Modules (giant robots) can be selected to explore the planet. Many planets have towns or people living on them, which can be talked to to uncover information. Different quests are assigned to find items necessary for progression.
There is no system of currency in Cyber Knight. Instead, many defeated Berserkers leave behind "NeoParts", which can be brought back to the Swordfish's lab. Analysis of these Neo parts unlocks enhances statistics (endurance, agility, accuracy, etc) for the Modules and new weapons for them to carry. The six Modules are unique in statistics, and each pilot carries different skills.
Combat takes place in turn-based combat on a 6x6 squares field. Seen from the side view, three modules can be positioned in relation to enemies to attack, using various melee and long-ranged weaponry. Ammunition is unlimited, but each module also carries consumable attacks known as "options". Each Module has two sets of hitpoints: one for the pilot and one for the module itself. If either reaches zero, the module is destroyed.
The party carries 10 each of repair kits and first aid kits, which must be restored by returning to the Swordfish when not in combat. These kits, as well as options and defeated pilots or modules can be replenished.