The events that happened before the first game's story are still largely a mystery, filled in by bits and pieces thanks to the Seven Crowns' Character Stories and to a large extent, the 7th Anniversary Story Event, Dive Astrum: Nanatsu no Negai to Sousei no Zankyou.

This section will be updated once in a while when new information is out.

Dive Astrum: The Seven Wishes and the Echoes of Creation

The creation of a new world

Senri Mana gathers a team of seven of the world's most brilliant geniuses and creates an organisation under the United Nations called WISDOM, with the goal of creating a highly-advanced VRMMORPG named "Legend of Astrum". These seven geniuses, who lead WISDOM, are then known as the Seven Crowns, each with their own title.

A short introduction of the Seven Crowns (in no particular order):

Mosakuji Akira (Queen Labyrinth)

A world-renowned doctor, who is also a highly capable programmer. It is implied that all seven of them are good at programming, but Akira's skills stand out even among them, being only behind Mana (and possibly Sora and Vision's Empress).
She once turned Sora down when he recruited her as she was in a dark place at the time (details are scarce, but it is hinted to have something to do with her father's death), but she met Yuuki by coincidence and after seeing how there's still some good in this world, regains her once cheerful and optimistic self and decides to take up Sora's offer.
The reason she joined the project is because she wants to make people smile like Yuuki did, and because she believes virtual reality games have the potential to treat what modern medicine can't (i.e. mental scars).
It is quite often mentioned that Akira is the only ethical and morally-good Seven Crowns member (the rest are morally-grey, except for Mana, who is outright labelled 'evil' by some characters).
In charge of the design, creation and placement of objects in Legend of Astrum.

Rajkumar Rajnikanth (King Leap)

A professor from India, who also happens to be the strongest man on Earth and is a formidable boxer. A battle-maniac that is always on the lookout for strong people to fight.
Most characters address him as "Rajiraji" because they find his name hard to pronounce. Some characters also address him as simply "Professor".
Some examples of how powerful Rajiraji is: he was able to destroy a car with only his fists, and Mana, who is also a very powerful fighter, says that Rajiraji is the only person capable of killing him in the real world.
Fluent in Japanese. Speaks very politely (with honourifics) but also in an arrogant tone.
The reason he joined the project is so that he can get stronger (since there's no one left in the real world that can give him a challenge).
In charge of the world's setting and item designs (eg. costumes, physical features of the Races, etc) during the development of Legend of Astrum.

Utsushimi Neneka (Metamorph Regnant)

A spymaster under the Cabinet Intelligence and Research Office (CIRO, essentially Japan's equivalent of CIA and MI6).
Described as looking like an elementary schooler, even though she's 24 years old.
Highly intelligent and has very good acting skills and a very good understanding of the human psyche, being able to play all kinds of roles. She's always wearing a 'mask' and Akira said that Neneka has never shown her true side to any of them.
Obsessed with wanting to be able to mimic anyone. This is also the reason why she joined the project.
Acts cold to most people, but is hinted to have a slight tsundere attitude (especially towards Masaki, who she treats haphazardly but obviously cares a lot for).
She has a personal bodyguard named Kurumazaki Masaki. Masaki is a fairly high-ranking officer within the Public Security Bureau's Third Foreign Affairs Division.
In charge of NPC design during the development of Legend of Astrum.

Christina Morgan (Regina Geis)

An entrepreneur, model, professional gamer (she runs her own pro gaming team as well), etc based in America (unclear if she's American). Has her hands in a bunch of businesses, and was recently approached to become an idol producer. Has wide connections.
Has a unique view of the world, believing there needs to be an 'absolute' in this world. Christina looks up to Mana (to the point of essentially worshipping him) because Mana is a genius among geniuses, even among the Seven Crowns, and is worthy of being the 'absolute' label.
Never breaks her promises. This is also where her title comes from, as 'geis' in Irish can refer to a 'vow' or 'obligation' ('regina' is Latin for 'Queen').
Like Rajiraji, fluent in Japanese.
While the Seven Crowns members are not particularly friendly with one another in general, Akira and Christina see each other as friends.
Unclear what her job during the development of Legend of Astrum was. She was seen testing out gameplay mechanic and making suggestions to improve on them. When Sora mentioned passing the job of debugging the game field to her, she made it clear that debugging is one of the areas she dislikes (Sora doesn't do things without reason, so this implies she's a capable programmer too).

Senri Mana (Kaiser Insight)

The CEO of an IT mega corporation named "Thousand Group", and an extremely famous and powerful celebrity. The one who first proposed the idea of making Legend of Astrum and gathered the other Seven Crowns.
Said to be a "genius among genisues" even within the Seven Crowns. His computing skills are top-notch and second to none.
Male, but passes off as female in the public eye, as well as within Legend of Astrum. The only ones that know his gender are his family and the Seven Crowns.
Some characters have described him to be outright evil, though at certain points in the story we can see that isn't exactly an accurate description. A very complicated character.
Speaks in a polite tone with honourifics, but is arrogant and treats everyone like they're beneath him. That said, he does show Sora some respect. Mana does not bother remembering the names of people aside from those he acknowledges (eg. the other Seven Crowns and Sumika).
While the Seven Crowns don't get along particularly well with one another in general, Mana and Akira absolutely cannot stand each other. It is hinted that this is because of Akira's good nature being in contrast with his, as well as Mana viewing Akira as an equal (though he would never admit to it).

Natsume Sora (Great Guidance)

The oldest of the Seven Crowns and is their de facto leader, assigning tasks to them. Nicknamed "Elder" among the Seven Crowns (Akira had been callin him Elder since when she was his student).
It's unclear what his actual profession is, but it is heavily implied he specialises in mechanics and medicine. He was also Akira's "teacher" (the game doesn't say if a school teacher or he simply took Akira under his wing), and Akira says his medical skill and knowledge are above hers. He is also well-respected in the medical world enough for the hospital which Sumika was at to contact him in desperation to see if he can do anything for the terminally-ill girl.
There's still a lot of mystery around him, making him the most mysterious Seven Crowns member after Vision's Empress. Homare mentioned a terrible event that happened approximately 12 years ago; she speculated that this event caused him to age more quickly from the stress as his actual age is not as old as his appearance suggests. He himself said that he once came to know "the abyss of this world" and said it was during then that his wish (which is still unknown) was born; it's assumed this is the same event as the one Homare mentioned.
He is a serious man of few words, but when he speaks, he does so in a stoic and wise manner, like a sage.
A running gag is that his personality changes and becomes a silly, loving father's when it comes to his daughter (though he still speaks in the same stoic manner). For example, Rajiraji was in charge of the design for all settings (eg. lore, costumes, etc) but Sora requested to let him do the elven village's. When Rajiraji showed Sora his design for the elves' costumes, he expected Sora to give a wise opinion on it as usual, but Sora simply asked "isn't this too revealing?", to which Rajiraji realised Sora planned to let his daughter become the elven village's shrine maiden.

??? (Vision's Empress)

The most mysterious of the seven, there's barely information on her. Even the rest of the Seven Crowns know hardly anything about her, not even her looks and her real name.
Not physically present at the lab during the development of Legend of Astrum, though she did play her part in the development process and also took part in the video call meeting, though she never spoke a single word and did not show her face, instead replying with static noises (hilariously, Christina was able to understand what she's trying to say with the noises, which shocked Akira).
Strongly implied to be non-human. The existences of ghosts, vampires, angels, etc have been confirmed so this itself is not surprising, but it's unclear if she's a supernatural lifeform or some advanced AI.
Interestingly, her title slightly strays away from the pattern used for the rest of the Seven Crowns' titles.
Her Astrum avatar's silhouette is shown in the official artwork for the 7th Anniversary story event, which depicts her as a rather well-endowed woman in a long formal dress with her shoulders revealed, and with long hair, pointy ears, horns and wings that resemble a Dragonfolk's. There seems to be a flower on the side of her head (possibly one on each side, we only see her side profile). It has been pointed out by players that her appearance slightly resembles Minerva's.
She also appears briefly (albeit with her face 'obscured') in the epilogue of the 7th Anniversary story event, secretly visiting Sumika's comatose body after Akira and Sora left the room. She thanks Sumika as she is able to 'test' thanks to her, and is able to get closer to her wish.

The Seven Crowns (or more specificlly, Sora) got their hands on "a piece of technology" that allowed people to log into Legend of Astrum, but they weren't able to make use of it at all until they came across a young, terminally ill girl named Yukisame Sumika by chance, who happened to be compatible with the device, allowing players to dive into the virtual reality world through their souls. They then used, with Sumika's consent, her as a test subject during the development of Legend of Astrum.

Halfway through the project, Akira wanted to stop everything and free Sumika, as she knew that Sumika is dying very soon. The rest of the Seven Crowns disagreed, and Sumika herself wanted to continue, as she would soon die whether she did so or not, and would rather see to the completion of the 'new world' they were trying to create. Akira reluctantly gave in and the group pressed on.

Eventually, the development was finally complete. Sumika had the honour of being the first player to step into the final product (the Seven Crowns' way of thanking her). It is then revealed that Sumika is the 'goddess' Ameth (the original 'goddess' of Astrum that Kokkoro's elven tribe worships, not the "Ameth" that we know, who is just Fio who happened to get Ameth's body). Ameth spent some time exploring Astrum (Rajiraji gave her the Leap ability so she was able to teleport from place to place) and was genuinely happy and excited since she is wheelchair-bound in real life and Astrum is a world she could only dream of.

At some point, Minerva showed up and greeted her, curiously asking her what her wish is, to which Ameth replied that she would like to "guide players visiting this world", letting players know what a wonderful world Astrum is. Minerva 'granted' Ameth's wish by bestowing her with wings and turning her into the first Navigation Fairy. Ameth was excited for a moment, before sadly telling Minerva that she doesn't have a lot of time left. In response, Minerva created small Navigation Fairies based on Sumika's soul (the one shown in the cutscene is Fio), and said they are the Navigation Fairies born from her heart that will eventually guide people in this world, and told her to think of them as her little sisters. Ameth thanked Minerva for granting her wish and allowing her wish to go on forever (since her sisters will carry on her role in her stead after she passes).

Present time: A new crisis that threatens the existence of this world

Time has passed and the main part of the 7th Anniversary story event now takes place in present time (i.e. during Arc 3). I know this page is for the first game's story, but I'll write out the remaining of the story under this page as well since they're connected.

In present time, Fio and Yuuki wake up in Astrum to find themselves in a rather odd scenario: Fio woke up in her original Navigation Fairy body instead of Ameth's, and a certain area of Landosol, which is usually crowded with people, is silent with no one around at all. "Ameth" (with lavender hair and wings in perfect condition) suddenly appears before them, who smiles at Fio. Fio demands to know who she is and what is going on, but before "Ameth" could answer, the three are wrapped in a blinding light like the ones that happen when Fio-Ameth shows Yuuki and players "dreams".

After the "dream", Yuuki and Fio wake up and see Labyrista, together with Neneka and Christina, fighting against "Kaiser Insight". The group initially thinks this "Kaiser Insight" is a fake, but the three Seven Crowns quickly realise this "Kaiser Insight" is the "real" deal, being a copy of the Kaiser Insight during the development of Legend of Astrum, who has access to broken skills not available in the main game. They are cornered, but "Ameth" shows up all of a sudden, and sends them some data with a UI menu showing up asking if they want to "restore". The three select "yes" and their avatars are restored to the ones they used during the development of Legend of Astrum, the Alpha Avatars. With their newfound powers, they take out "Kaiser Insight" with ease.

However, Neneka tells the group that she used her familiar Gregor to scout the area and discovered that the copies of the old Seven Crowns are causing mass destruction around Astrum, so the three set off to deal with them, but not before Labyrista tells Yuuki to take care of "Ameth". Meanwhile, "Ameth" introduces herself to Yuuki and Fio as Yukisame Sumika, the player that this "Ameth" was based on, and one of the test subjects that took part in the development of Legend of Astrum. Sumika further explains that the chaos happening right now is her fault, as someone outside is trying to steal her data (i.e. memories), since her memories of the development process are extremely valuable. She froze her account long ago and went into what was supposed to be an eternal slumber, but someone reactivated her account, which caused a massive bug in which the pre-release Legend of Astrum is overwriting the current Astrum. Sumika then asks Yuuki for a favour: She wants him to erase her so that the culprit can no longer steal her memories and cause further damage to this world. Yuuki however, refuses. An "earthquake" occurs and the blinding light covers them once again, and Yuuki and Fio are shown another piece of Sumika's memories.

After the flashbacks, Yuuki and Fio wake up to find out that the landscape has been replaced with the test field during pre-release Legend of Astrum, proof of the overwriting's progress. Meanwhile, the Seven Crown copies that Labyrista, Neneka and Christina were fighting teleport away together with the "earthquake", gathering in one spot and have merged to become one monster with all the Seven Crowns' (except Vision's Empress) abilities. Sumika is also losing more and more of her functions and can hardly speak. The monster targets Sumika, but Neneka and Christina show up and save them. However, the monster uses all 6 Seven Crowns abilities at the same time, cornering Neneka and Christina. Before it could grab Sumika, Labyrista shows up in the nick of time, bringing the real King Leap, Great Guidance and Kaiser Insight with her, and the 6 Seven Crowns stand against the monster.

Before they start fighting the monster however, Yuuki says he will be the one to defeat that monster. All of the Seven Crowns brush aisde his idea, saying that he's too weak to fight it... all except Kaiser Insight, who suggests that it's possible if Yuuki gets back his original ability, an ability designed specifically to defeat the Seven Crowns. Sumika isn't able to do anything in her weakened state, but she sends Fio some data and leaves the rest to her. Fio, who already had memories from Legend of Astrum, is able to pass the data to him with the help from Sumika, waking up his original ability, the Anti-Seven Crowns and Anti-Princess Knight Sword.

The Seven Crowns members help fend of the monster's attacks, clearing the path for Yuuki. However, the monster attempts to use a powerful spell to blow everything including itself to smithereens. Before it is able to do so, a long-distance attack stops it in its tracks, allowing Yuuki to stab the monster with his sword, putting an end to it.

This however, also puts an end to Sumika's time in Astrum. She asks for Fio to continue using her body and take over her role as the goddess Ameth, saying it would make her happy to know Ameth—the body born from her—is still travelling around in this world from time to time. She then gifts the two with the last fragment of her memories: the completion of the development of Legend of Astrum, Sumika's short but memorable journey in the game, and her encounter with Minerva. After the flashback, Sumika has disappeared and Fio bids farewell to her big sister, returning to Ameth's body.

Epilogue

One of ex-WISDOM researchers who used to be part of Legend of Astrum's development is attempting to steal Sumika's data, but the last portion is taking forever. The security alarm is activated all of a sudden, and the researcher immediately makes his escape. He runs into Sora, who praises his quick decision to run and advises him to give up the data. The researcher ignores Sora's advise and gets out of the lab.

Outside, he runs into Akira—smiling but obviously angry underneath the smile—who praises him for choosing this timing to make his move since the Seven Crowns cannot move freely (as they are now fugitives due to the events in main story's Arc 3) but tells him that he did the one thing he should not have done, which scares the researcher. He continues to run, but not before Akira throws and latches a tracker onto him without him knowing, and shares his location data with the rest of the Seven Crowns in the messaging app she made specifically for them.

The researcher continues to run, cursing the fact he ran into two Seven Crowns. He remains optimistic he can make his escape and attempts to send the data to the organisation he is working for while running, but realises that his terminal cannot connect to the network. Mana appears behind him, laughing at how he didn't even notice Akira's little parlour trick. The researcher is shocked to hear Mana's voice, attempts to recruit Mana to his organisation, saying that they can provide a hideout for him, and saying this is surely a good trade for the data of some guinea pig he doesn't even know the name of. Mana instead spurns his attempts, and tells him that the organisation he works for—which the name Mana doesn't even remember because it's not worth remembering—no longer exists, as the Seven Crowns have already crushed it and there's only one bug left to squash. The researcher runs away screaming.

He continues to run, knowing everything is over but he can still get away in his getaway car that he parked nearby. However, he runs into Christina, who slowly approaches him. The panicked man takes out a taser gun and warns her to stop, but Christina confidently walks towards him. He fires and misses, and quickly decides to get into his car. Christina warns him that she wouldn't recommend getting into the car now, and before he even realises what she meant by that, Rajnikanth lands on the car from out of nowhere, turns it into scrap metal and tells him that he should have prepared an armoured vehicle at the very least if he wants to escape. Rajnikanth's appearance scares the hell out of him, and before he could even react, Rajnikanth breaks his arm. Christina and Rajnikanth jokingly wonder aloud if they should each "test out the durability of the man's legs".

Before they could do so, Neneka shows up and stops them. The two jest about giving Neneka the "honours" in respect to her showing up here despite being busy, and Neneka return the joke by saying it would be interesting if she arrests the two of them together with the researcher. After the two leave, the researcher heaves a sigh of relief, thinking the danger is over. However, Neneka tells him to not be mistaken, as all she wants from him is information and she won't hesitate to hurt weaklings if necessary, and says she'll be looking forward to find out whether the scales will tip towards the weight of his crimes or the weight of his life, causing him to pass out from shock.

Back at the lab, Akira sneaks in to take a look at Sumika, who remains in a coma. Sora is already by Sumika's side, and the two medical experts discuss her condition. Their conversation reveals that there is no doubt that Sumika should have died a while ago, and that her current condition is nothing but a miracle. They speculate that Sumika ran into Minerva on that last day, and Akira wonders if Minerva granted her wish. Sora tells her that it is unlikely as it goes against Minerva's "rules" back then (this was before Minerva decided to grant the wish of the Princess), and it is more likely that Minerva used Sumika as the test subject for granting wishes. Sumika's lack of changes is a proof that Minerva's "test" is still ongoing, and Akira thinks of it as a good thing, giving them time to improve and find a way to save her.

After the two leave, Vision's Empress shows up by Sumika's side, leaving the comatose girl a cryptic message:

"Yukisame Sumika. You have my gratitute.

"Thanks to you, I am able to 'test'. I am able to get closer to my wish. That's right......"

"It's thanks to your life."

"——May the blessings of the sun and stars be with your soul."

In Fio's Character Stories (in present time), Fio was summoned to the real world all of a sudden, in Sumika's body. It is implied that this happened due to a safety program made by Minerva, allowing Sumika's body to safely get under Akira's protection (i.e. Minerva is entrusting Akira with Sumika's comatose body and Fio is the 'pilot'). After Akira found Fio (Sumika), she helped Fio get back to Astrum using mimi, but Sumika herself thanked Akira right before going into a coma again, proving that she is still somehow alive in some way.