The characters used for the Church follows the author’s naming convention of having it named after a place and adding its quality. The name Amakusa is derived from the real life Amakusa, a series of islands in Japan, off the west coast of Kysushu, and their secrecy is a reference to the Kakure Kirishitan of that bygone age.
The kanji that is used can be interpreted as Amakusa-Style Christian Weird Doctrine or Amakusa-Style Church of Distinct Doctrines. The character used for sei (凄?) traditionally means dreadful, threatening, weird, uncanny. In the English language, weird can be used as a synonym for peculiar, unique, or distinct. However, it only applies when the name of the Church is written down in text, as the Church's pronunciation is simply called Amakusa-Style Christian Church. Due to the different way the furigana is used in comparison to other churches in Toaru Majutsu no Index, this wiki will use the term Amakusa-Style Remix of Church or the Amakusa Church for short for all articles.
On 1549 Francisco de Jasso y Azpilcueta arrived in Japan, and later, on the island of Kyuushu began preaching Roman Catholicism, where the future Amakusa Christians would form. However, at the height of Japan’s isolationist foreign policy, during the Edo period, the Japanese Christians were left to fend for themselves as they were persecuted. The Christians were forced into hiding, but the Japanese government countered by using Fumi-e to reveal to reveal practicing Christians and sympathizers.
According to Tatemiya Saiji, the Amakusa Church was established during the Tokugawa Shogunate of the Edo Period. They were most likely formed after the Shimabara Rebellion led by Amakusa Shirou, though this is just speculation. As a result of the continued persecution, they hid Christianity behind Shinto and Buddhist symbols. However, they ended up mixing with other religions until they couldn’t even tell which parts originated from which religion. Although originally a branch of Roman Catholicism, due to the influences of other religions and the need for secrecy, the Amakusa Christians were now completely different from the Roman Catholic Church, and has now become a unique fusion-style Christian sect.
The Amakusa Church was apparently in a state of decline, and apparently prospered when Kanzaki Kaori became the Priestess, as according to Laura Stuart they were only able to survive because of Kaori.
When Kaori was born, she was chosen as the Priestess or Supreme Pontiff of the Church. She was extremely blessed and had the uncanny ability to succeed no matter what she does. Eventually she saw that when something fortunate happens to her, something misfortunate happens to others in turn. However, those people who are misfortunate, still admired her regardless, and through hither, Kaori became disillusioned with her sect, blaming herself for their misfortune. This led her to despise the concept of luck and fortune as her fortune in turn only bring misery to those around her from what she can see, as it has been mentioned in the novels she no longer wants to see innocent people rushing to protect her, dying in the process, and saying with their last breath that it's alright as long as she's fine.
Three years before the start of the series, Kaori defects from the Amakusa-Style Remix of Church to the Anglican Church, and became a part of the Church of Necessary Evil. Although, her love for her comrades remained. After her defection, Tatemiya Saiji became the Substitute Supreme Pontiff. Because of her defection, the Amakusa blamed themselves for their weakness, and tried to become stronger, taking into mind the teachings of their Priestess, and specifically, to reach out to all the abandoned.
By the time of their introduction into the timeline, they are well known enough for even people like Orsola Aquinas to seek refuge to. However, they Church still wanted to join Kaori, as is the reason why Saiji wears St. George’s Cross on his shirt, to show that they want to join her.
As noted, the Amakusa Church is a fusion of Christian, Buddhist, and Shinto principles, forming a unique religion far removed from Roman Catholicism. It also take concepts of other countries' cultures ever since the Edo period, and have fused sword techniques of all ages to create their own unique style. As consequence to this, the Amakusa Christians are able to use any with ease, whether it is a Japanese sword or a Western broadsword. This probably also includes battle styles as well as naval tactics, as the Amakusa Christians mimic fireboats as what the English Navy did against the Spanish Armada in the Battle of Gravelines. This also extends to their clothes, not wearing any standard religious garb, allowing them to blend in with people, such as Academy City, changing an outfit if they see it fit.  The Amakusa Christians basically learn about all the surroundings and think of the most suitable ways to blend into the surroundings. With that regard, they have no problem with blending with another culture.
It is unknown how large the Amakusa Church is, though it can be assumed that it is small enough for it to be hidden. There are at least 52 combat-ready Amakusa Christians, and is reportedly based in Kyushu, though can probably move albeit limited due to the 47 Portals of Japan . After joining the Church of England, the Amakusa was given residences in a Japanese street in London.
Prior to joining the Church of England, the Amakusa Christians seemed to have no regard for their relationship with the other churches as they only cared to follow their own tenets that were set down by Kaori, including giving refuge to Orsola Aquinas, who threatened the Christianity due to her ability to decode the Book of the Law.
After joining the Anglican Church, the Amakusa Church is used in order to tether Kanzaki Kaori into the Church and not betray them, as Laura Stuart explains, through the use of benevolence and protection for the sect instead of violence. The Amakusa Church then begin carrying missions for the Church, though since they are still just a small sub-branch, when the need arises, the Church can cut them off or use them as scapegoats.
The Supreme Pontiff is the one who leads the Amakusa Church, and as the name indicates, is equivalent to a Pope. If Kanzaki Kaori is any indication, they are chosen at birth,  and apparently become the old leader dies, essentially making the leader for life. If the leader abdicates the position, a Substitute Supreme Pontiff leads the Church, though it is unknown how one becomes a Substitute Supreme Pontiff. There are apparently no other positions in the Church, no sense of hierarchy, and little to no sense of seniority, as Isahaya seems to show.
The Amakusa Christians, during battle, act like one entire unit. Other than Isahaya, whose granddaughter is Itsuwa, the Amakusa Christians, despite seemingly having no familial relations, act like they are truly close together like family, and barring Saiji and Kaori due to their positions, the members call each other by given name.
- Kanzaki Kaori (Current Pontiff (Priestess))
- Tatemiya Saiji (Substitute Supreme Pontiff)
Hundreds of years of persecution and secrecy have given the Amakusa Church a unique identity that is a combination of, but separate from its orthodox influences. These influences range from Roman Catholicism, the main denomination that the Amakusa Church derived from, Buddhism, and Shintoism, two religions that have existed in Japan prior to the arrival of the missionaries. The Amakusa Christian’s specialty is secrecy, since they’re Christians whose nature is to deceive others; they hide the teachings of Christianity inside Shintoism and Buddhism completely, and use rituals and techniques as part of their greetings, diet, and behavior in their everyday lives. They cover all their tracks so that others won’t even notice their existence. These teachings have been passed down from generation to generation.
Since the Edo period, the Amakusa Christians, have been studying other cultures, as such they have acquired have fused sword techniques of all ages to create their own unique style. This also extends to other melee weapons, not just swords. These weapons range from swords like the Western broadsword and Saiji's trademark Flamberge, to Japanese swords like Kaori’s Nodachi and the Bateren-Dedicted Toushou (Transparent Crystal) sword by Kanemitsu. This also includes other melee weapons such Itsuwa’s Friulian Spear, to axes, mazes, and daggers, as well as ranged weapons like crossbows and longbows. The Amakusa Christians usually sacrifice the sharpness of their weapons for ease of carrying it secretly, though can strengthen them if they so choose.
Moreover, the Amakusa Christians can use their steel wires as a weapon, as exemplified by Kanzaki Kaori and Itsuwa, though, they can also use it to support their magic. For instance, the 3-dimensional magic array they created to protect London from a bunker cluster missile attack perpetrated by Princess Carissa during the English Civil War.
The Amakusa Christians also have in their possession, a submersible wooden vessel and ships, which can be changed into and back to paper using the relationship between paper is made from wood and that ships are made from wood.
Unlike the human wave tactics that the vast Agnese Forces, the Amakusa Christians, with its at least 52 combat-ready members,, have been shown to be much more focused on teamwork and unity. In their battle against Acqua of the Back, their teamwork was a necessary component to survive against his attacks, with each movement an important part of their formation. They used a tactic that moved the focal point, or the main target of Acqua of the Back, which in this case is Itsuwa, when Acqua of the Back pursues the center, which will then scatter into the crowd, and disappear, and just when they prepare to ignore the center, Itsuwa will again be the focal point. They also incorporate their teamwork into their magic, having a body strengthening spell that requires the members to move properly in their formations.
They are shown of being capable of guerilla and ambush tactics, as shown when they waited for Orsola Aquinas to fall into the hands of the Roman Catholic Church and catching them unawares to retrieve her. As well, as being able to steal her away while fighting the Roman Catholic Church for two days. Moreover, due to the fact that they have been hunted and persecuted for generations, the Amakusa Church know the weakness of large organizations, such as the Roman Catholic Church, and act accordingly to their movements.
The Amakusa Christians also specialize in island combat.
Passed down from generation to generation, the Amakusa-Style Remix of Church is an organization, whose magic is unique due to their incorporation of many religions. This allows them to pass restrictions that are other present in one religion, such as the harming of deities in Christianity being forbidden, but is manageable, though frowned upon, in Shintoism.
Due to their persecution in the past, the Amakusa Christians specializes in secrecy, deception, and stealth. This extends to their magic. They do not use ordinary methods of magic, such as through plain magic arrays or chanting. They hide rituals behind the mundane, such as greetings, diet, and behavior, and hiding their magical items behind ordinary objects, such as kitchen utensils, underwear, paper, etc. Their intricacies of using codes and logos through the ordinary, originating from several abandoned religious rituals, choreographed repeatedly, showed their mastery of Idol Theory, and as a consequence making them unpredictable.  Moreover, due to the teachings of Shintoism, where it is taught that gods reside in everything and any object can become a magical tool, the Amakusa church often uses this idea by creating spells out of the objects at hand. However, because a different god resided in each object, a single object cannot be used for various different kinds of spells.
Even when not in combat, the Amakusa Christians train themselves, having a designated method to cook their designated food, else their reactions will retard. The Amakusa Church is a religion that uses all sorts of religious rituals in their everyday life, including sleeping, bathing, and walking. Since the situation is different, they can only eat a limited number of things.
Magic that can be attributed to the whole of the ChurchEdit
- Communication spell: Tatemiya Saiji used a floating paper balloon that allowed him to communicate with Orsola Aquinas. 
- Miniature Copy Pilgrimage
- Binding charms: The Amakusa Christians used some form of charmed rope and talisman to bound and gagged Orsola Aquinas, which are easily dispatched by Touma’s Imagine Breaker.
- Healing Magic
- Paper–Wood Transformation Magic: Uses the relationship that wood is made out of paper, and that certain things are made out of wood, to allow them to transform wooden objects into a bundle of paper or vice-versa.
- Damage transference charm: Charms the clothes on an Amakusa Christian to transfer damage on their body to their clothes, weakening damage that is inflicted on the user.
- Steel Wires: Nearly invisible steel wires that are used in a variety of manners, and can be formed into a magic array.
- Nanasen: Uses 7 wires to attack the enemy, like Kanzaki Kaori.
- A Punishment of a Killer: Through the use of the entire combat ready members of the Amakusa Church, each of them has 7 steel wires on their fingers, creating a deadly web of 350 wires surrounding the opponent. When used, it instantaneously bind the opponent’s body together with extreme force exerted throughout the wire. Red mist then expands and engulfs the target, like an inescapable prison. The mist surrounding the target would expand twice or thrice, like a continuous bomb explosion in water. Each explosion triggered another chain of explosions. Each of the explosions continued to chain up. This is a spell that allows each wire to have symbolic features of being a person’s lifeline, and then punish the person that destroyed these wires. This is an ancient thing, a spell that any religion has, no matter the culture, in other words, no matter what kind of defensive spell it belongs, it can’t block this Curses of the Fallen. It is referred as a sure-kill technique.
- High-Speed Escape Spell: Exact use is unknown, but is used for retreats.
- Insert-From-Behind Recovery Spell: Requiring the use of teamwork, the Amakusa Christians strengthen each other by touching each other’s back. They continue to change formations as they fight, the moment they move and cross each other, their comrades will pat each other on the back, recovering the body functions and immediately get stronger. It’s not a spell that a person alone can do, it’s a group-exclusive movement spell that works for their comrades.
The spell’s effects will be heightened, with the Feng shui effect of a pulse like a sleeping corner or rest point.
With their comrades helping, the effect of the increase in mobility increases, allowing them to be able to match a Saint’s speed.
- Saint Destroyer: Requires the Amakusa Christians to set-up a formation, with the attacker at the center, the Saint Destroyer is a magic attack that works on Saints alone. It appears as blueish-white purple electricity, causing an explosion, and the electricity forms into a Cross, the weakness of Saints through Idol Theory, as Saints have a body that is similar to the Son of God who was crucified on a cross and was pierced. Explosions continue to occur after the magic attack is dealt.
The Saint Destroyer, in theory, is only effective against a Saint, and has no offensive abilities against ordinary magicians.
It was created by the Amakusa Christians after the departure of Kanzaki Kaori in order to understand the burden of being a Saint, and in theory, surpass whatever she feels as a threat.