For twenty years, Attera has been under attack from monsters spawning from anomalies called Dusk Circles. To fight those monsters, people with the Star God Brand, called Disciples, are gathered and trained in a school in Fort City. The Dusk Circles are said to appear because of mankind's desires. Eight such circles forming the Pandora Labyrinth are known to exist: the original one, which is still inactive, and one for each of the seven deadly sins. The Disciples formed at the Academy are the first line of defense against the monsters, but they cannot enter the labyrinth since the energy inside nullifies their Star Power.
The player takes on the role of a new male Disciple whose name may be entered manually or chosen at random. On the day he arrives at the Academy, he meets with two other newcomers, Fuuko and Chlotz, whom he saves from a stray monster. Once at the Academy, they are to be assigned a rank, to know if they are standard Disciples or elite, and have their Ether count measured. All three are found to be elites, Fuuko is even an S rank, the highest possible rank. The protagonist is only A rank, but his Ether count is off the charts. That high amount of Ether (tens of times the average) makes him a special Disciple called God's Gift. This will enable him to create an Ether field which allows him to enter the Dusk Circles and make it possible for other Disciples to accompany him and use Star Energy inside.
Like its predecessor, Conception II: Children of the Seven Stars is divided in two parts: the city and academy, and the dungeons. The player moves to the different areas in the city by choosing them on a list. Each area has its own purpose: the dorm is where the player edits the party and manages the save data, the church is where new units are created, and the Academy is where most events occur. To create Star Children, the hero must perform a ritual known as classmating with one of the seven heroines. Classmating requires BP, which is gained in bonding events and by meeting certain conditions in battle. As the hero's Ether and an heroine's Star Energy are combined inside a device called a Matryoshka womb, Star Children of various classes are born. Each Star Child is either male or female and has his or her own abilities. The strength and maximum level of a Star Child is influenced by the bond (mood and intimacy) the hero has with the selected heroine.
In the dungeons, the player explores a randomized labyrinth with a party of up to four units: the hero and one of the heroines form the main unit, and three groups of three Star Children may accompany them. The enemies are displayed by icons that change depending on the foe's strength; the weakest enemies can be defeated without fighting. In battle, the units act in turn and are placed either in front, behind or on one of the sides of an enemy. Each enemy has a weak spot, a direction from which more damage is dealt. Attacking from dangerous spots fills the chain gauge; when the gauge fills enough, the monster's turn gets delayed. Another aspect of battles is the Ether level: depending what actions are performed, this level will rise or lower.
As with many dating simulation games, Conception II: Children of the Seven Stars has multiple endings depending on the different relationships developed throughout the game.