A prologue consisting of four parts has been added in Fire Emblem: Shadow Dragon. It chronicles the fall of the kingdom of Altea, prior to Prince Marth's departure to the island of Talys where he appears to be in Chapter 1: 'Marth Embarks' (and the beginning of Fire Emblem: Shadow Dragon and the Blade of Light and Fire Emblem: Mystery of the Emblem). This set of scenarios is only available in Normal Mode, however, and will automatically be skipped should the player choose to play the Hard Mode, automatically selecting the canon course of events (Not killing Gordin, using Frey as the decoy and not recruiting Norne) in that case.
The basics of combat are explained throughout the prologue if the player opts to enable the in-game tutorial. Also, two of the Shadow Dragon exclusive characters, Frey and Norne, can only be recruited in the prologue chapter, although the former is not canonically present in the main game.
—Marth to Gra soldiers
At the dead of night, Prince Marth is shocked to find himself surrounded by Gra soldiers in his own castle's corridor. He soon learns of his father's defeat at the hands of Gra, his own allies, and is implored by his sister, Princess Elice, to flee the fallen castle ahead of her.
- Enemy number: 4 (Gra)
- Enemy types: 2 Fighters and 2 Soldiers (one of them occupying the yellow tile).
—Elice to Malledus
Marth is joined by two Altean cavaliers, Frey and Abel. Together, they head towards the gate to meet up with Sir Jagen, and the cavalier Cain who had accompanied the fallen king's entourage on that fateful day. Meanwhile, Elice orders Malledus to catch up with the young prince and accompany him as his advisor.
- Enemy number: 6 (Gra)
- Enemy types: 1 Fighter, 2 Archers and 3 Soldiers (one of whom occupies the yellow tile).
- Frey - Cavalier
- Abel - Cavalier
- Jagen - Paladin (Since he joins at the end of the battle, he cannot be used before the next part)
- Cain - Cavalier (Since he joins at the end of the battle, he cannot be used until the next part)
"Thus Prince Marth escaped Altea Castle with Sir Jagen and company at his side. However, this success would mean little to him once he learned the cost.
The boy's woes were just beginning."
Cain delivers to Marth the king's final request: Marth must rise as Falchion's remaining heir and restore peace to the continent of Archanea. After a brief skirmish with Gra soldiers, Malledus arrives to join Marth (as a NPC) and explains to him Elice's decision to stay behind to ensure the boy's safety. She, too, believes that only Marth can save the land.
- Enemy number: 10 (Gra)
- Enemy types: 4 Soldiers, 2 Archers, 2 Fighters and 2 Mages (one of them occupying the yellow tile).
- Residence: 5 houses. (Each with a resident offering gameplay advice.)
—Malledus to Marth
"Marth and his knights took refuge in a forest near Altea's borders, lying low while they waited for the right chance to escape the kingdom. Before long, the enemy grew less watchful: the time to slip away had come.
Still, the prince could not quell the sadness in his heart for his sister Elice."
Malledus tells Marth that Elice wanted him to seek refuge in the island of Talys, and so they must pass by a prison in order to reach the docks. At the prison, Marth meets the Altean archer, Gordin, who was being held captive and forced to dress up as one of Gra's soldiers. Before the group manages to make it to the docks, however, they find themselves surrounded by Gra forces from all sides, one of them led by King Jiol of Gra himself. At this point, Malledus suggests sending out one of Marth's knights as a decoy to mislead Jiol's troops, if Marth is to have any chance of survival. Despite Marth's protests, one of the five Altean units volunteers to carry out Malledus's plan and thus supposedly perishes after fulfilling the task. (Canonically, Frey sacrifices himself but ultimately survives.)
If Marth rushes to the marked fortress instead of sending a decoy, the northern door will not be opened unless all of his allies are killed.
An alternative scenario occurs if Marth actually mistakes Gordin for an enemy and kills him off. In that case, Jiol's troops will not show up, and instead, the enemy Captain will have the door opened to lure Marth out and finish him off himself.
- Enemy number: Several (Gra) enemies from the start. Two sets of Pegasus Knights will appear as reinforcement at the forts on the west side of the battlefield. Somewhere in between (if the player does not kill Gordin as an enemy), Jiol's troops will emerge from the south, but at this point in the game, they appear to be impossible to defeat.
- Residence: 2 houses and 1 village (no thieves).
- Items: Iron Bow (dropped), Steel Bow (village)
- Gordin - Archer (Talk with Marth)
- Draug - Knight (Cannot be used in this battle as he joins at the end).
- Norne - Archer (If two or more ally units are gone by the end of the prologue; decoy included. She cannot be used in this battle as she joins at the end)
- The Door Key that Malledus gives to Marth in the opening cutscene of Prologue IV cannot be discarded, or traded to another character, presumably to prevent an unwinnable situation.
- The map of Prologue II and Prologue IV are both contained within the maps of Star and Savior and The Battle for Altea respectively.
- Despite this, The map for Prologue I does not appear inside Star and Savior, despite both taking place in Castle Altea, and more specifically featuring the castle's throne.
- The map for Prologue III also does not appear as part of either map. This is explainable, however, as it existing somewhere between the 2 chapters' locations.