The game builds on the game mechanics used in the previous two Game Boy Advance Fire Emblem titles—Fire Emblem: Fūin no Tsurugi and Fire Emblem—but takes place on a different world. Set on the continent of Magvel, the plot focuses on royal twins Princess Eirika and Prince Ephraim as they investigate why a longtime ally has chosen to invade their nation's borders and the sudden appearance of monsters all over Magvel.
Though it received positive reviews, The Sacred Stones was criticized for making only superficial improvements over the previous game. Despite these comments, the game received an average rating of 85% on Game Rankings.
The Sacred Stones introduces several new concepts and revives some old ones used in previous Fire Emblem games. The most notable change is the map system, which allows the player to have more control of how much experience the team gets and thus how they level-up.
A notable difference that separates The Sacred Stones from previous Game Boy Advance Fire Emblem titles is the use of a navigable world map, a mechanic first used in Fire Emblem Gaiden. Rather than limit the ability to train units and buy items to story battles, the ability to traverse the world map allows players more freedom in choosing how to play the game. It is possible to purchase weapons and items by visiting shops at points scattered across Magvel. Basic iron weapons and low-level tomes can also be purchased at an inflated cost from the armory in the supply caravan before battle, and units can pull items from the supply caravan during battle when standing adjacent to the main character. The Sacred Stones features monsters, all of which appear only as enemies, which are battled in some chapters in the main game. It is also possible to enter "Skirmish" battles against monsters unrelated to the story.
Trainee classes were introduced in The Sacred Stones, which precede some of the previously basic classes. These include Journeymen, Recruits and Pupils. Characters that are in a trainee class gain more experience than usual, and when they reach Level 10, they stop gaining experience and can class-change at the beginning of the next battle without the aid of an item. As with other classes, players can choose one of two basic classes to change into. After certain criteria are met, the trainee classes have a third class-change option, which is a slightly stronger version of the original trainee class.
The skill system was first introduced in Fire Emblem: Seisen no Keifu, and made a return in The Sacred Stones. In The Sacred Stones, some unit classes have a unique skill that gives it an advantage in battle. For example, the Bishop's "Slayer" skill triples a weapon's might when fighting monsters. The skills cannot be removed from the unit.
Fire Emblem: The Sacred Stones takes place on the fictional continent of Magvel. The storyline is unrelated to any of the previous Fire Emblem titles in the series.
Magvel is home to six nations of diverse leadership. With the exception of Carcino, a newly established republic, each nation shares a history of 800 years since the War of the Stones and are responsible for their own Sacred Stone. The nations have enjoyed a long-lasting peace until the Grado Empire suddenly invades its neighbor, Renais. Prince Ephraim of Renais, one of two main characters of the game, leaves Renais to fight back Grado's invasion. However, he goes missing and Grado's forces fast approach the vicinity of Renais castle. Princess Eirika, Ephraim's twin sister and the initial main character, leaves Renais, along with her loyal knights, to seek help from their allies, Frelia.
Eventually Eirika reunites with her brother. The two discover that Grado intends to destroy the five Sacred Stones of Magvel, with both Frelia and Grado's Sacred Stones already destroyed. Ephraim decides to take the fight to Grado, while Eirika and Innes, the prince of Frelia, leave to warn the remaining two Sacred Stone nations, Rausten and Jehanna. Eventually Grado falls to Ephraim, but the true villain behind the war remains to be fought—Grado's imperial prince Lyon, Eirika and Ephraim's longtime friend, who has been possessed by the Demon King of legends.
Reviewers have praised the level of attention that the game gives to the storyline and each individual unit, but have commented on the frustration that can be caused by some gameplay features inherent to the series, such as the fact that character death is permanent. The game has also been criticized for not improving upon gameplay mechanics as much as expected from a sequel. As well as lack of innovation in gameplay, reviewers have also noted that the presentation has not changed much from Fire Emblem. Overall, reviewers acknowledge that the game has the same solid gameplay and replay value that was present in Fire Emblem, despite the lack of originality.