Ephraim is engaged in guerrilla war against Grado in an attempt to divert Grado troops from their invasion into Renais, concurrently with his father's death. During this time, he encountered the manakete Myrrh and rescued her from Grado forces. Blaming himself for his inability to aid his father in his time of need, he wonders where his younger sister went and traveled to Renvall with his companions Forde, Kyle and Orson. Upon disposing the commander inside, Orson reveals his true colors, forcing Ephraim, Forde and Kyle to flee. Tirado later spread false news about Ephraim's capture to lure Eirika into Renvall.

Upon falling into Tirado's trap, Ephraim heard of the news and rushed to his sister's aid, joining forces with her and defeating Tirado. Upon returning to Frelia, Ephraim decided to go to Grado to get answers.

In his path, Ephraim first approaches Fort Rigwald, with its defenders attempting to hold out a Frelian siege. After rescuing Tana whom was captured while looking for his group. Ephraim and his forces kill the commander inside, forcing the garrison to surrender. Upon interrogating one of the prisoners, he learns about Duessel's reaction to the war, and heads towards Bethroen to assist him.

Upon arriving at Bethroen, Ephraim assists Duessel in repelling the forces sent to kill him, and Duessel later joins Ephraim on his journey. Ephraim hears rumors about a phantom ship destroying anything in its path in the Grado's seas, and goes out with his group to determine if the rumors are false or not. The rumors are true, and with Dozla and L'Arachel's help, destroy its crew. Upon arriving at Taizel, Grado forces led by Caellach surround them, but Caellach is quickly recalled to the capital by Riev. Riev supplements the army there with monsters, and Ephraim is shocked that the monsters are not attacking Grado soldiers. Despite this, his group manages to push on to Za'albul Marsh, where he encounters Myrrh, who tells him not to kill Selena. He is forced to however, as she refuses to move aside due to loyalty.

After dispatching her, he finally arrives at Grado, where he besieges the castle, killing Vigarde. He later reunites with his sister in Jehanna, and takes the throne back from Orson, before heading to Rasuten and finally Darkling Woods to stop Fomortiis from destroying Magvel. After Fomortiis is destroyed, he returns to Renais and rebuilds the nation with Eirika. Marrying Tana or L'Arachel if he has an A-Rank support with either of them and uniting Renais with Frelia or Rausten respectively.