The story of Scars of Mirrodin takes place in the plane of Mirrodin. Mirrodin is an artificial plane, so the number of artifacts and cards relating to that permanent type is larger than normal and mechanically reflects the themes already explored in the previous sets. The set describes the conflict between two major factions - one being Mirrodin, and the other being the invading forces of Phyrexia. Cards aligned with these two factions are watermarked. The two factions are also mechanically separated, with the Phyrexians dealing largely with Poison, Infect and Proliferate while the native Mirrans use mechanics already introduced or similar to those of the original Mirrodin set - Imprint, Indestructible, Charge Counters the new Metalcraft mechanic, as well as Mana Myr and Spellbombs.
The story also revolves around several planeswalkers. Elspeth Tirel returns while a new planeswalker by the name of Koth is introduced who appears to be of Vulshok heritage and thus would be native to Mirrodin. Venser and Tezzeret are also involved in the storyline. Being set on Mirrodin, the expansion features themes and settings already known from that plane. For example, creature types and tribes of these such as Leonin, Vampires, Loxodon, Elves, or the Human tribes of Vulshok, Auriok and Neurok. Artifact creatures such as Golems and Myr are also present.