Nephtyke is a story-driven Manga RPG with a Queue-based battle system. Players can enjoy the game’s story in the form of reading a manga. However, when a battle would occur within the story, players cannot continue reading, and instead get to experience that battle directly through a queue-based battle system. Nephtyke’s battle system lets the players direct the flow of the battle, making the characters act based on their liking. In battle, each character's action is displayed as a dynamically generated manga panel. Once the battle is over, the game takes all the panels generated during the battle and creates new pages to allow the player to continue reading the story.

Just like a normal manga, Nephtyke as a Manga RPG is divided into volumes and chapters. Players can read each chapter to enjoy the story, while each battle within the story is enjoyed through the game’s battle system. In battles, players get personalized battle pages to fill in the missing story parts crafting a unique experience for each player.. Additionally, each battle has missions which allow players to unlock challenge battles, extra chapters, and upgrade points, letting them enjoy the game’s intricate battle system beyond just the regular story mode. Using upgrade points, players can make the characters stronger or unlock more actions to make the dynamically generated pages further to their liking. The Challenge battles are additional battles designed for those who wish to test their skills. Finally, the extra chapters are unlockable short stories which give players insight into Nephtyke’s characters daily lives.

Nephtyke has a queue-based battle system, which is a twist on a classical turn-based RPG battle system. Each turn represents a chunk of time within which characters can perform multiple actions. Instead of deciding each character’s action when it’s their turn to act, the player queues-up action upfront, adding a more tactical approach to the battle and giving the player the feeling of acting as a Battle Director for the manga’s story. At the start of a turn, each character is assigned Time Points, based on which they can queue-up a certain amount of actions to execute. The amount of Time Points each character is granted, but faster actions consume less Time Points, meaning faster characters would perform more actions in the same turn. Once all the actions have been queued up, characters execute the queued-up actions based on their combined order. Each battle action is shown as a dynamically generated panel, based on the attacking and defending characters, and which action was selected for them. The game stores each of the generated panels so that it could generate new manga pages at the end of the battle. At the end of the battle, the game generates new manga pages using the dynamically generated panels throughout the battle and adding it to the story pages allowing the players to enjoy the story further with personalized battle pages which are the result of their effort.

Nephtykes story follows Sorel, a young Tectodian who made a promise to his deceased mother that he would protect their village in her stead. He continues to guard his village for years from the assaults from the neighboring Tectos Kingdom, but one day, a grander duty falls upon Sorel as a mysterious group of mercenaries attempts to kidnap one of the villagers.