A youth has grown up as one of the royal children of the glory-seeking nation of Nohr. Though their father has forbidden them to leave the castle, they still live a happy life with their four siblings. However, when they finally are sent to the outside world, it is on a mission to Hoshido, a peace-loving country that Nohr has plans to invade. There they learn that they were born to the Hoshido royal family, and were kidnapped by Nohr as an infant. A Nohr princess named Azura was taken hostage by Hoshido in retaliation, and has been living in a similar situation to the protagonist. With war looming on the horizon, Azura and the protagonist choose to side with their family in Nohr, and reform the nation from the inside.
Conquest is one of three versions of Fire Emblem Fates, the others being Birthright and Revelation. In this version, the player controls their fully customizable avatar as they lead Nohr's forces in strategic battles against the corrupt forces controlling the nation. Gameplay is similar to early Fire Emblem games, with more challenging gameplay and no opportunities to grind for money, items, or experience in between storyline battles. In addition to the Classic and Casual modes featured in Fire Emblem Awakening, this game contains Phoenix Mode, in which defeated allies are immediately resurrected on the following turn. Players pick one of these three modes at the start of the game, but may choose to permanently switch from Classic or Casual to a less difficult mode later on.
Supports also return from Awakening, allowing characters to build their relationships as they fight alongside each other. Two characters of the opposite sex may get married and have children once their relationship has progressed enough, and Conquest also includes the possibility of a same-sex relationship if the player chooses the male protagonist.
A feature called My Castle allows the player to build and customize a village that can contain various helpful buildings, such as shops that sell weapons or healing items. The village can be upgraded with resources collected through StreetPass, and it is also where StreetPass battles are held. Winning a StreetPass battle allows the player to recruit one of the defeated opponent units into their own army, and a shop in the village allows players to purchase other special units called Einherjard.
Players may purchase DLC that allows them to play through the Birthright and Revelation scenarios as well.