The manga begins in a snowy setting, with several Pandora already wounded and strewn across the ice. Yumi Kim and Elize Schmitz are portrayed clearly exhausted while facing a Type S Nova, a Nova type previously unknown. They comment on it's speed, power, and it's more powerful Freezing field as the snow hinders their mobility. Just as Yumi is about to be killed, Kazuha Aoi appears and deflects the Nova's attack. She tells the Pandora that while the type S is a new threat, she has a solution for it. Kazuha is next depicted as performing the skills Accel and Tempest turns; High End Skills that no one else has used before. Yumi is awed by it and thinks back to the first day they met.

The manga shifts back to the first day of Yumi's 3rd year at Genetics. She and Elize are outside when a newly arrived Kazuha runs into Yumi (with Elize commenting that Kazuha would need at least 3 weeks to recover from the impact of Yumi's breasts). The characters introduce themselves, and the senior Pandora learn that she is the granddaughter of Aoi Gengo.

Title Notes: Zero was first published in コミックヴァルキリー (Comic Valkyrie) volume 37 (May 2012)

The episode starts with a scene in the year 2053 showing a young Scarlett Ohara and Gengo Aoi observing Gengo's 10 year-old granddaughter Aoi Kazuha going through some Pandora training exercises. The scene then shifts to the L. Bridget estate during the year 2022, where a young Gengo Aoi and a military commander convenes with a then 18 year-old Howard L. Bridget to discuss the creation of a super-soldier project to fight the Nova threat. Two projects, codenamed Valkyrie and Pandora, were proposed. The time then returns to the year 2060, right after the events in the first episode. Yumi, Elize and Shion Nayfield are shown discussing the second-year winner of the spring carnival and how she would be a good addition to the Numbers. Kazuha then shows up and announces that she would be taking the place of the second-year winner, much to the ire of Yumi.

Title Notes: コミックヴァルキリー (Comic Valkyrie) volume 37 (May 2012) contains episodes 1 and 2 of Freezing: Zero

Grand Canyon Chevalier Central Headquarters identity is reinforced. The simulated Type-F Nova is revealed. Radox is revealed to be the commander of the Chevalier and that Aoi Gengo was his rival for the position. The Seiga company is revealed to be an upstart that built the simulator. Kim Yumi's nickname is revealed to be "the Gorilla of the West". It is revealed that Aoi Kazuha is the only Pandora cadet allowed to live off-campus, and she commutes from her home with her brother. Aoi Kazuha is revealed to be extremely close to her younger brother, Aoi Kazuya. Kotou Saeko is revealed to be #1 in her year at East Genetics. Kim Yumi is revealed to be Student Council President at West Genetics. It is revealed that Kotou Saeko, after failing to reach #1 in her freshman year, transferred from West Genetics to East Genetics. Baek Mi-Ryung challenges Kotou Saeko to a duel. Kazuha Aoi reveals that personal duels are against the rules.

Kim Yumi and Elize Schmitz meed Aoi Kazuya at the Aoi siblings home. It is revealed that the Aoi siblings left their grandfather's house for independence, and they live off Aoi Kazuha's stipend for being a Pandora cadet. Being a Pandora cadet was also the only way that their grandfather, Dr. Aoi Gengo would let them leave.

The Faylan generator is revealed to be more powerful than nuclear generators, and something that powers the simulacrum Novas, and created by Seiga Heavy Industries.

Kotou Saeko is defeated by Baek Mi-Ryung in their duel. While Kotou is faster, Baek is more powerful.

Title Notes: This chapter was published in コミックヴァルキリー (Comic Valkyrie) volume 38 (July 2012)

While Baek Mi-Ryung is conversing with Kim Yu-Mi, Kotou Saeko counter-attacks, and misses, hitting the control panel for the Type-F simulacrum Nova, sending it out of control. Kim sends Elize Schmidz to warn the rest of the Academy and Sister Margaret. Saeko does not listen to Yumi's instructions and acts on her own instead of in concert with Miryung. After Yumi rescues Saeko, she reprimands her for not being a team player. Yumi is then knocked out by the simulacrum. Saeko and Miryung face the simulacrum alone and together. Aoi Kazuha, having been ordered not by Yumi to interfere, now takes action because Yumi is out of it. She takes out the simulacrum single-handedly and introduces the first ever high-end skill, and showing everyone a very large and unheard of number of stigmata activating.

Title Notes: This chapter was published in コミックヴァルキリー (Comic Valkyrie) volume 39 (September 2012)

Arnett McMillan is on the verge of turning 14, the entrance age for Chevalier Genetics Academies. She is travelling with her father, Keith to San Francisco (where Chevalier have a base). On the way, they pick up two lewd hitchhikers, glasses-girl Cynthia and topless Kate. When they arrive, Keith reveals to Arnett that she has 80% compatibility with stigmata. She however doesn't want to become a Pandora.

Arnett and her father travel on from the motel, where Arnett thinks Kate and Cynthia are lesbians, as she catches them in bed together naked. Hijackers attempt to take Keith's truck, and blow it off the road with an RPG. Keith is rescued from falling off a cliffside trapped in the truck when it is revealed that the two hitchhikers are actually US Chevalier Pandoras Kate Avelli and Cynthia Ruth.

Title Notes: This chapter was published in コミックヴァルキリー (Comic Valkyrie) volume 40 (November 2012)

Elizabeth Mably is introduced, first in her loving family home, with her family. Then it shifts to the pre-Genetics training camp that prepares Pandora-candidates-select (pseudo-Pandora) prior to stigma implantation. It shows how hard boot camp is, and reduces the cadet candidates to numbers, and not names, with no deference given to the social status the girls had prior to entry, or their relative immaturity. It shows that Elizabeth is willing to stand up to authority if it treats girls badly, and get punished for it. Elizabeth is revealed to be part of the 28th Genetics Welcome Group, and part of the #3 platoon of that group. Her boot sergeant is the Korean Chevalier Park Se Mi.

Boot camp continues. Second Lieutenant Park singles out recruit GM160 Elizabeth Mably for special intense attention. A failure for any individual Pandora candidate select is a failure for the entire training platoon, so Mably's mistakes get extra training for all. It also gets her special additional lessons. First Lieutenant Hilda says she should be a bit kinder.

Title Notes: This chapter was published in Web Comic Valkyrie (chapter preview)

Title Notes: This chapter was published in Web Comic Valkyrie (chapter preview)

Title Notes: This chapter was published in Web Comic Valkyrie (chapter preview)