Bleach: Execution is set in an alternate universe where the events of the Bleach Manga played out dramatically differently. A thousand years ago, Genryūsai Shigekuni Yamamoto fell in battle during the purging of the Quincy, taking the Emperor of the Vandenreich, Juhabach Gudmundur, with him. The Vandenreich survived however, hiding in the shadows of the German wildnerness, far from the prying eyes of the Shinigami. Here, the Quincy slowly rebuilt their numbers, being guided in this endeavor by Juhabach's son, Fenrir Gudmundur, the second Vandenreich emperor. Genryūsai Shigekuni Yamamoto's gifted son, Senrei Yamamoto, former captain of the 9th Division, became the New Captain Commander in his father's stead.

Meanwhile, a naturally talented Shinigami named Sōsuke Aizen was born, and rapidly rose to the position of Lieutenant of the 5th division. He became obsessed with a device known as the Hōgyoku, and began to attempt to create one. His experiments went wrong, however, and his Hōgyoku misfired during creation, killing him and his subordinates. 5th Division Captain Shinji Hirako was caught in the blast which devoured most of their division's barracks, though he escaped with only a lost arm. Ashamed at his failure to protect his squad, he retired, and his position was taken by a talented 2nd squad member, Kisuke Urahara. Together with Kirio Hikifune, captain of the 12th division, he founded the Shinigami Research and Development Institute, recruiting convict Mayuri Kurotsuchi to join him in his project. When Kirio Hikifune was recruited to the Zero Division four months later, Mayuri Kurotsuchi took her position as captain of the 12th Division.

Rōjūrō Ōtoribashi was challenged to a Captain's duel by Senrei's childhood friend, Sasuke Kazuhiro. Sasuke easily killed Rōjūrō, and took his place as third division captain. Kenpachi Kiganjō, Captain of the 11th Division, fell in combat, and his seat was taken by a talented Shinigami from the 9th Division; Kensei Muguruma. Retsu Unohana died due to a generic condition, and her student, Izumi Aoihime, took her place as 4th Division Captain. Jūshirō Ukitake's illness finally claimed him, and talented 6th division Lieutenant Keiichi Sanjou became captain of the 13th Division. Byakuya Kuchiki, Captain of the 6th Division, after the death of his beloved wife, fell ill. Retiring to become head of the Kuchiki family, he left his position to his sister, Rukia Kuchiki.

Without Aizen taking over Hueco Mundo, Lord Baraggan Louisenbairn remained in charge, ruling over the vast deserts of his kingdom. However, one of his Vasto Lorde subordinates became power hungry, and planned a coup de'tat. Although he failed, with his dying breath he managed to catch Baraggan off guard, and shattered his mask. The hollow King of Hueco Mundo was strong to survive his mask shattering, however, and he became an Arrancar. Experiencing how dramatically his powers increased after his mask was removed, Baraggan began to convert the strongest of his empire to Arrancar.

The process failed at first, as no other hollow was strong enough to become a perfect Arrancar naturally. However, Baraggan began to experiment, trying to create a Hadō like technique to stabilise hollows during the conversion process so they didn't lose their might. The greatest of his Vasto Lordes, Plata Margana, volunteered to be used as a test subject. The spell was successful, converting her into a perfect Arrancar, but at a cost. She reverted to a childlike state, and took her place as Cero Espada. After seeing what happened to Plata, Baraggan began to modify his spell, and rapidly perfected it, allowing him to create an endless supply of Arrancar to fuel his army. Baraggan rapidly began to convert other noteworthy Adjuchas and Vasto Lordes from his army, however, and established La Legión, his mighty Arrancar army. To house this mighty force he had created, Baraggan created Las Noches, a massive castle separating his mighty Arrancar legion from the lesser hollows of the outside world.

The fabric of reality is splintered. Strange creatures known as blanks have been bleeding through into the world of the living; Souls that have fallen out of the circle of transmigration and lost their memories. The appearance of the blanks is a long standing natural occurrence, small numbers of them occasionally escape from the Valley of screams and begin to hunt down their lost memories. However, these events are very rare and only ever happened in small numbers. Lately, however, thousands of blanks have been showing up world wide, travelling in swarms world wide, clearly seeking something. Unconfirmed reports have surfaced about a strange new species known as the Specters appearing with the Blanks, only showing up where their numbers reach the tens of thousands. These Specters look humanoid, and have been reported to devour the blanks. Nobody knows what they are after, or how they got here. Only time will tell...