Soul Energy is the energy used by Pandora and Nova to fuel their abilities. This energy is derived from extra dimensional sources, and is somehow tied into the Transcendent Will. This energy is channeled through the Stigma. The energy is also a double edge sword as drawing too much energy has the potential to transform a Pandora into a Nova.
Soul Energy is at the core of all Stigmata, which Gengo Aoi describes as the life force found in all beings. Elements such as air and water also possess this unique "soul energy" as well. Soul Energy is similar to any other form of energy. It is used and fades, and when all of a creature's life force or soul energy is exhausted, they can no longer function and die as a result. 
Soul Energy can be distributed among beings to heal injuries or corrupt and kill them.
Project Soul SitmgaEdit
- Main article: Stigmata
When Gengo Aoi was created his daughters, the Legendary Pandora, he equipped them with the Legendary Stigmata, which is the diamond stigmata that manifests on their trachea when they fight seriously. The Legendary Stigmata were the first Stigmata Gengo developed. They were the result of Gengo's attempt to convert this life force energy into a numerical value that could be harnessed by humans, code named Project Soul Stigma.
When Gengo made the Legendary Stigmata for his daughters, the first one he developed, used by Cassandra Aoi, was able to house millions of Soul Energy. However, Cassandra's body, both human and Nova, could not handle that power, so her body collapsed and needed to be placed into stasis. Gengo reduced the production of the Legendary Stigmata for his next children: Teslad, Windy May, and Lucy. With each child, Gengo had to continue reducing the power of the engine because their bodies could not handle it. Teslad was put into stasis. Windy May could be released only periodically and Lucy, the most stable at the time, still required multiple tune-ups. Gengo's success with the Legendary Stigma and managing Soul Energy came with Chiffon Aoi, who was perfectly stable.
After Chiffon's success, Gengo continued to siphon from Maria Lancelot's body to produce mass-produced Stigmata, and Gengo severely reduced the output of Soul Energy per Stigmata as they were implanted in compatible humans. In comparison, the soul energy output of Legendary Stigma, even Chiffon's, is equivalent to the output of roughly 100,000 regular Stigmata. 
Between humans, Pandora, Legendary Pandora, and different forms of Nova, many sentient living being process soul energy differently. Each human possesses one soul energy, which can last for an average of 100 years, which is the normal human life span, until the energy fades and humans die a natural death. 
- Main article: Legendary Pandora
After the early failures of Project Soul Stigma with the Legendary Pandora, and Lucy, Gengo installed his daughters with Vital Frames, which awards Soul Energy a visible numerical value and allows them to to better control and convert their soul energy into usable duel. Chiffon, however, did not require these Vital Frames. The Legendary Pandora are all capable of absorbing Soul Energy from Pandora and energy attacks. When the Legendary Pandora run out of soul energy, it is assumed that they can die as any other living being, but as shown during the 13th Nova Clash, they seem to simply "shut down" and are rendered unconscious. The Legendary Stigmata developed by Scarlett Ohara was enough to fully empower and restore their lost energy supply.
Project Soul Stigmata led to the production of mass produced Stigmata for ordinary Pandora, but Pandora use Stigmata differently than the Legendary Pandora. The Legendary Pandora produce or absorb massive amounts of soul energy and expel it to their liking. As explained by Garatolos Eluka Nova, Pandora use the soul energy produced by their Stigmata to take their own singular soul and compress it hundreds of times for their tremendous abilities, such as High End Skills or to regenerate from their injuries. The rare few can do so thousands of times. Pare are subsequently able to reset and replenish this energy. All Pandora execute this process, but they are unaware of the true mechanics behind their abilities. 
The process is easier, the attacks are stronger, and the feats are superior for more experienced Pandora, hence the difference in strength between a first-year Pandora and a third-year Pandora. The same applies individuals with more powerful Stigmata or Pandora more compatible with Stigmata. Such is the case of the Busters, whose bodies could house seven Plasma Stigma and the world-ranked Pandora, who each possess miniature Legendary Stigmata, also known as the Heroic Stigmata. For Pandora using the same Stigma Material, the individual who could better use the soul energy produced by the Stigmata to compress their soul would be the superior Pandora. This is how Isuzu Sawatari was able to easily defeat Petty Layner. The former was better at compressing her soul and maximizing the potential of her Plasma Stigmata. 
By contrast, Marin Maxwell, who had two Stigmata and minimal compatibility with them, could only compress her soul energy at twenty percent of the average Pandora, this making her severely weak.  The same applied to Tiziana Caldani who had to retire because her body was never truly suited for Stigmata. 
- Main article: Transcendent Pandora
Transcendence allows Pandora to draw out the maximum power of their Stigmata to make a stronger stigmatic material that increases one's combat abilities. For infantile Transcendent Pandora, their soul compression rate is a tad inferior to individuals with at least seven Plasma Stigma.
Transcendent Pandora are capable of compressing their Soul Energy ten thousands of times with Rana Linchen, the strongest of them, able to compress her six Stigmata at least 20,000 times. Pandora are able to absorb soul energy from their surroundings, which makes soul compression easier. As with the case of the Pandora of Platoon 13, absorbing soul energy from the Elcarium dimension is enough to trigger transcendence and reactivate transcendent abilities more quickly and efficiently to maintain a heightened level of combat. 
Those with Stigma Bodies are able to manipulate soul energy from Nova and Pandora easily. The Legendary Pandora are such individuals as they all have Stigma Bodies. Kazuha Aoi was able to compress her own soul to unseen levels at the time, which led to the invention of High End Skills. For Kazuya Aoi, he could absorb thousands of Soul Energy from Cassandra and dispersed it to three Pandora, inducing transcendence in two and giving all three the power to destroy 5 Pandora-Type Nova. 
Arcadia Aoi absorbed massive amounts of Soul Energy from the air and then from the Legendary Pandora. Instead of collapsing under this power, Arcadia's body actually transformed to better house this energy.  She can continue absorbing this energy without any immediate drawbacks, but if she does not use the energy, she must release it eventually and return to her normal teenage form.
- Main article: Nova
Unlike humans, Nova are born with several hundred souls, but they cannot generate soul energy. Rather, they strictly absorb soul energy from the environment, people, or Nova, house it and expel it by compressing their hundreds of soul at once thousands of times per their needs. The most powerful Nova can compress thirty years of soul energy at once. 
With each evolution of the Nova, subsequent forms are able to absorb more and more soul energy making them stronger than their previous incarnations. The Nova traditionally store this energy in a particular core in the center of their chest, akin to a human heart. Destroying this core expels all of the Nova's soul energy, which kills them.
On Pandora and Limiters, Soul Energy can be safely infused to heal injuries as far as restoring limbs to full dexterity, but at the cost of accelerating the aging process. Because most all Pandora cannot heal their own injuries, the Stigmata is most often artificially stimulated in a controlled environment to trigger limb and injury regeneration. Pandora Doctor Elize Schmitz specializes in this area.
When Soul Energy is released by a Legendary Pandora to heal individuals with Stigma, they can even resurrect the dead as in the case of Roxanne Elipton. Incidentally, Roxanne is the only non-Legendary Pandora capable of regenerating her own limbs and other injuries by compressing her own soul. She does not need outside Soul Energy or artificial stimulation of the Stigmata to do so.
- Main article: Nova Form
The reason a particular compatibility is required for humans to accept Stigmata is due to the consequences of too much soul energy being injected into the body. The summarized consequence is Nova Form.
Stigmata only produce ten units of soul energy, and because humans only have one soul and are only meant to have one soul, even that small amount is enough to kill them. For the Pandora compatible with Stigmata, even they require limitations. Some Pandora can house only two, as in the case of Attia Simmons but others in extremely rare circumstances can house up to eight as in the case of Isuzu Sawatari. Kazuha Aoi, who had a Stigma Body, could house 20. Men as well require a similar level of compatibility to be Limiters and all so far can only house one Stigma.
Even more special compatibility is required for Heroic Stigmata, Plasma Stigmata, Legendary Stigmata, and the Legendary Stigmata System. For example, Charles Bonaparte who possesses five Stigmata has two of which that are Heroic Stigmata. She has a 75% compatibility rate with her regular Stigmata but a 48% compatibility rate with her inherited Stigmata. Furthermore, the untested Legendary Stigmata System is not safe for most any Pandora to use, aside from Su-Na Lee due to the Stigma purity of the battle armor. Ordinary Pandora assuming any of these special materials are at a higher risk of Novalization and may die. 
Infusing any human or Pandora with an overflow of Soul Energy can overwhelm their bodies and reduce them to Nova Form. This effect similarly applies directly to Assimilation Nova Form attack Nova can inflict on Pandora. They induce Pandora with a calculated level of Soul Energy to convert them to Nova Form and subsequently control them. The only "benefit" of Assilimation-Type Nova Form is that if the Nova Form Pandora is knocked out, they can return to their human form. When the infused soul energy infused into humans or Rounders is not calculated, they can all be corrupted and rendered them berserk.
For Legendary Pandora, their bodies required continuous reduction of power with each sister because their bodies couldn't handle the overflow of soul energy. They require the Vital Frames to maintain stability and control. Chiffon Aoi could deliberately overload her body with Soul Energy to induce Nova Form, and she retained her sentience. However, after evolving too much, she knew she could not return to her human form. Due to Chiffon's lack of Vital Frames and reduced soul energy production, absorbing the explosive soul energy from Amelia Evans during the 11th Nova Clash completely dissolved her body. 
If a Pandora or Limiter tries to compress their Soul Energy or attempt to produce Soul Energy from their Stigmata to levels they cannot handle, they will not experience immediate Nova Form. Rather, they may experience Stigma Overload, a lesser form of Novalization, which can still result in death. Such is how Isuzu killed her victims as a Genetics Pandora as she deliberately pushed her opponents to a power level they could not handle. If a Pandora does not die from Stigma Overload, they are are able to recover but if the damage is too severe, they are not able to continue active duty. Such happened to Margaret Lindman after pushing her new Pandora Mode to its zenith to win the 6th Nova Clash.
Limiters are not afforded similar luxuries as Pandora when they experience Stigma Overload. When a Limiter exerts too much Soul Energy and Novalizes, visibly only their skin cracks, but the body undergoes much more serious destruction that they never fully recover from. During the E-Pandora Rebellion Arc, André Françoise did just that to ensure Elizabeth's Mably's victory over Charles. While he was able to recover and resume active duty, his eyes and vision are forever scarred and he requires special visors to see.
- It can be assumed that Limiters compress their singular Soul Energy to produce Freezing fields, but this is unconfirmed. In addition, it is unknown what merits the "strength" of a Limiter and their Freezing Field: individual skill, individual compatibility, or the strength of the Stigma they inherited from the Pandora they are bonded. As such, the strength of a Limiter would be proportional to the strength of his Pandora.
- It is currently unknown out the Valkyries compress or expel soul energy, but the process is connected to the Faylan Generators.