Stella Deus é um jogo de RPG tático baseado em história em que o jogador controla um grupo de personagens escolhidos durante o curso da história e em eventos paralelos. O mundo é navegado usando um mapa do mundo superior usando navegação ponto a ponto, com um sistema de datas mostrando o tempo necessário para chegar a um local selecionado. Juntamente com as missões da história, as Cidades podem ser visitadas, nas quais os personagens podem personalizar e criar novas armas e armaduras, vender equipamentos existentes em troca de dinheiro e comprar itens como poções de cura. Em acampamentos montados em uma jornada, os personagens podem trocar armas e armaduras, equipar itens como poções de cura e amuletos benéficos para batalhas futuras. Itens especiais usados no nivelamento de personagens também podem ser criados pelo jogador. Juntamente com as missões baseadas em histórias, há uma masmorra especial chamada Catacumba das Provações, onde os personagens podem lutar e ganhar níveis de experiência, aumentando suas estatísticas gerais. O número de níveis disponíveis na Catacumba aumenta à medida que os jogadores progridem no jogo. Cada personagem tem uma classe de personagem específica, que eles mantêm durante todo o jogo e continuam a subir de nível à medida que ganham pontos de experiência (XP). Quantidades mais altas de XP são concedidas por executar habilidades especiais. Junto com espadachins e arqueiros, existem alquimistas (magos), sacerdotes (curandeiros) e unidades que lutam usando a maioria das coisas, de machados a punhos. Most battles are triggered based on story events, and are completed when the stated object has been accomplished by the player, be it defeating all enemies, defeating a boss, or performing a specific task. At the end of each battle, the players gain a summery of their performance and spoils gained. The game uses the turn-based Replaceable Action Position battle system, much of which was carried over from the battle system used in Hoshigami: Ruining Blue Earth. Players navigate the field across a grid-based map, which can include obstacles such as bodies of water and high structures. Character positioning within the environment can be used to their advantage, such as an archer gaining higher accuracy when at a high point in the level. Character actions are arranged in a set order, and each character's weapon dictates their attack range. Each time a character performs an action, they gain experience points and additional Skill Points (SP) that can be used to purchase supplies or raise individual character stats. Three types of Skills can be equipped for characters: Action Skills, a special attack that player execute for a certain amount of Magic Points (MP); Support Skills, which grant passive abilities such as scaling higher obstacles; and Zone Skills, which grant passive abilities to both the equipped character and those in close proximity to them. Alongside Action Skills, two or more characters in conjunction trigger unique special moves called Team Attacks. The amount of damage done depends on how many characters took part in the action. Team attacks also increase the rewards gained at the end of battles. Characters' actions are governed by their stored Action Points (AP): a character's turn begins when their AP meter is at 100. A character's actions can continue until the meter reaches 0, meaning that they can move and attack multiple times within their turn. The amount of AP used with each action depends on the weight of the armor the character is wearing.

Stella Deus takes place in a world called Solum, which is slowly being swallowed by "Miasma", a mist-like substance that destroys all life it touches. Against this creeping apocalypse, several groups have developed responses. The Aeque Church, led by High Priestess Lumena, believes that the Miasma is God's will, sent to bring the world to an end, not with a bang, but a whimper. A warlord, Dignus, has taken to ravaging the countryside with his armies, imposing the law of the jungle: he who will not fight for his life does not to deserve to live. And finally, an alchemist named Viser is using Dignus's patronage to hunt the world's Spirits (polygonal creatures whose nature is unknown), draining their life-force to fuel his alchemic inventions, which he is sure will save the world. His friend and deputy, Spero, is the game's protagonist. Spero must make his way through this muddy political situation and see if he can save Solum.