Guilty Gear is... complicated. There are many story arcs going on, so we hope that this synopsis will help out. Enjoy!
Main Story: The Guilty Gear
The Destruction of Japan
In a distant future, mankind would discover the usage of magic and create significant advances to humanity overall. In America, a trio of researcher friends consisting Frederick, Aria and a man whose name was unknown up until now, would become several of the most prominent figures in this world. The three were good friends, but Aria held a rather fatal sickness that endangered her life, and both Frederick and his friend were getting desperate in order to find a way to cure her, even if they have to abandon everything. They decided to solve this and several other problems by spearheading the Gear Project, a project of creating enhanced humans with the power of magic. Aria would be the first of the Gears, with hopes that it would cure her of her sickness, while Frederick becomes the prototype.However, even at testing phase, a great tragedy occurred. This last friend witnessed an incoming assault of a supernatural being that would destroy the world and humanity with them if left be, and nothing could stop this supernatural power as it made its way through Japan. However, even if it caused him great regret, he unleashed what he thought to be the best method to quell this: Activate the first Gear, Aria, and have her unleash the destructive Gamma Ray into the force. This, unfortunately, came with a great price: The majority of Japanese people were obliterated, becoming endangered species. Aria was in complete anguish on what she was forced to do, and that friend vanished out of guilt, now being referred as 'That Man'. This did not sit well on Frederick, who wanted answers about what has happened. He quit his research job, and began to think that the Gear project was a complete sin, so he resolved to make amends of creating the whole project overall by destroying his creations.
And from that day, the scientist named Frederick was gone, and in his place, a powerful bounty hunter calling himself 'Sol Badguy' emerged.
The Crusades
Aria, now codenamed Justice, continued her existence by commanding all other Gears to help humanity. Sweeping changes has happened after the destruction of Japan, one of them being how America ended up falling from power and becoming insignificant. But what Justice noticed was that humanity started to mistreat Gears, treating them as nothing more than tools for killing. Unable to withstand this, Justice united all Gears and declared war on humanity.
To counter this, the Sacred Order of the Holy Knights were formed, guided by the old soldier Kliff Undersn. During the war, however, his son Testament was converted to the Gears side, and Kliff had to end his life. Fortunately for Kliff, he has several other loyal followers who would continue on his stead, with one of them being a young and idealistic knight that idolized him, Ky Kiske. And on the other side... was Sol himself.
Ky's chivalrous attitude clashed heavily with Sol's roguish attitude and they tend to bicker a lot. Eventually Ky was appointed as Kliff's successor and was granted the anti-Gear Outrage weapon, the Thunderseal. During his promotion, however, Sol quit the Sacred Order altogether, and also stealing another Outrage weapon, the Fireseal. This in turn made Ky overall bitter at Sol and swore to make him pay for his crimes. However at this point, Justice's attacks intensified and Kliff, in his age, was subdued and forced into retirement, necessitating Ky's leadership to keep humanity altogether. During this chance, however, Sol managed to confront Justice and fought her, holding her at bay, enough that Ky managed to mobilize the forces of humanity and seal Justice, ending the Crusades.
The Sacred Order Tournament
The world enjoyed peace for years. With the Sacred Orders disbanded, Ky then became an international policeman to protect mankind further, while still pursuing Sol for unanswered questions. However, around that time, invitations to a certain tournament were suddenly being handed down to many people, including Sol and Ky. The invitations sounded really fishy as they also involved pirates, drug addicts, assassins, serial killers as participants. That simply provided more reasons for the two to investigate this tournament.
Sol came out on top, and found out that this tournament was hosted by Testament, still under the thrall of Justice, whole plan to use the bloodshed created by the tournament to revive Justice and wipe out humanity. Sol defeated him, but Testament instead used his own blood to revive Justice. During her renewed rampage, Justice finally finished off Kliff in their 18th battle. Sol defeated her and prevented her doing further damage, which ended in Justice's death. Ky, who witnessed this ordeal and overheard about how Gears were treated, had a rude awakening that he might be following the dogma and the law too blindly. As Sol left and resumed his mission to wipe out all Gears, Ky tried to re-discover what the term 'justice' truly meant.
The Innocent Gear
A few months after Justice's defeat, the world was shaken with an announcement of a highly priced bounty, against a certain Gear that held immense power much like Justice. Many fighters, including Sol and Ky, investigated on this case further by participating in the ensuing race towards the bounty. Once again, Sol came out on top and he was once again greeted by Testament... except this time he's a lot more lucid and less destructive towards humanity in general, but he remained determined to protect this Gear.
After defeating Testament, Sol came across the Gear in question... a very pacifistic, innocent Gear who did not truly wish to fight and only wanted peace, and her name is Dizzy. But as a Bounty Hunter, Sol could not back away from the prize money and fought her, and in spite her pacifistic nature, Dizzy proved that she truly had destructive powers. Sol still prevailed, but this time, he couldn't bring himself to finish Dizzy off for some reason, speculated that he noticed that she could be his daughter from his relationship with Aria. After Sol left her, Dizzy was picked up by the Jellyfish Pirates where she would gain a lot of friends, while her prize money was handed down to the fighting chef Jam Kuradoberi.
Return of That Man
Only a short while after Dizzy was picked up by the Jellyfish Pirates, several mysterious figures started to make an appearance and generally causing chaos, spreading mistrust in humanity overall. That Man has somehow returned and possesses a certain knowledge about the future of the world. Sol decided that it's time to seek answers, but That Man's guardians such as I-No bar his way, but nothing could stop Sol, not even getting thrown into the past and killing his past self, avoiding time paradox. But even so, That Man were steps ahead of Sol.
However, I-No herself is something of a Wild Card, against That Man's wishes, she sowed chaos for nothing but laughs, and in particular, dropping Dizzy from the Jellyfish Pirate ship and causing her to once again enter a possessed mode, destroying things with her power. Not only that, she spread false bounties to many people, causing in-fightings here and there. Regardless, That Man had to reel her in at times.
Sol managed to calm Dizzy down for a bit and letting her return to the Jellyfish once again. But later on, Dizzy went down on her own. For some reason, however, her destructive instincts kicked about on its own and caused her to go berserk, but she's thankfully calmed down with the efforts of the captain, Johnny, and the passing-by Ky Kiske. Ky became acquaintated with Dizzy and helped her from being accosted by a certain Crow, who carried a clone of Justice for some reason. Eventually, his friendship with Dizzy grew more and it seemed that Ky finally found balance between law, justice and protecting people. Johnny then let Dizzy visit Ky more often and soon, their feelings bloomed... and they married.
The First Valentine Incident
Dizzy managed to lay an egg and gave birth to Ky's son, Sin Kiske. However, the Post War Administrative Bureau wanted to use him as a tool for their plans, and asked Ky to rule the kingdom of Illyria. When Ky protested, they threatened to expose the forbidden relations between him, a human, and Dizzy, a Gear. Ky reluctantly had to accept. And for that, he had to send Sin to the tutelage of Sol. However, this whole incident made Sin rather hateful towards his father and treating Sol as the better father-figure.
Later on, the world was shocked with the appearance of a Gear calling herself Valentine, and one of her power is automatically destroying Gears within her vicinity. Unfortunately, Dizzy was one such Gear in danger of being sublimated, so Ky sacrificed his Thunderseal to seal Dizzy in a stasis so she would survive, but as far as Sin is concerned when he heard this, it gave him more fuels to hate Ky. Regardless, Ky contacted Sol to help him with the problem with Valentine, and he complied.
Through trials and tribulations, Sol managed to defeat Valentine, even after he realized that she could be an incarnation of Aria, while Sin managed to stop overly hating Ky, though not completely.
The Second Valentine Incident
Still only a few months after the incident with Valentine, another figure announced her intention to declare war on the world. This figure also bore the name Valentine, but her full name is Ramlethal Valentine. Regardless, Ky would not leave this be and contacted Sol and Sin once again for help.
Ramlethal was not the only threat they faced, they also faced the enigmatic Conclave, that allied with Ramlethal, and an enigmatic boy named Bedman. However, they had help from Ky's war buddy and fellow King Leo Whitefang, and an innocent Valentine unit named Elphelt Valentine. With her help, they managed to subdue Ramlethal, with Elphelt and Sin trying to make sure that Ramlethal act more human just like Elphelt.
Eventually, after further investigating, it turned out that the Conclave is building a clone of Justice in order to rule the world. Thankfully, Sol, Ky and Leo received several aids, starting from the Jellyfish Pirates under Johnny, how That Man, in spite of Sol's misgivings, suddenly gave his aid to Sol to fight against the Conclave, and with Ky's permission and the help of Sol's friend Dr. Paradigm, they released Dizzy from her stasis and she helped out taking out this clone of Justice.
However, the war did not end completely on the heroes' favor. Bedman managed to sneak in and take That Man into custody, while it turned out that Elphelt, against her will, was revealed as The Mole working under Bedman's superior, Ariels, and she was quickly reprogrammed to oppose Sol. However, Sol managed to at least awaken a little of her more humane personality, and Ramlethal finally showed that she is now capable of showing human emotions, and together they swore to save Elphelt from this machinations, while Elphelt tearfully responded that she will wait for the rescue.
