So, in Angel Sanctuary there are two rather gay boys with a rather gay relationship which would have been canon if the REAL canon relationship wasn't one of those boys with his sister.
But! In the very first volume of the manga Kira declares that Setsuna was his 'woman' before he was even born, and it's this relationship: Kira's Soul, aka Lucifer, with the Organic Angel Alexiel, that is the sort of the... shadow romance of the entire manga. It starts in volume one and doesn't 'resolve' until the final volume, at the same time its existence doesn't really contain major spoilers. It's just a story that runs parallel to everything else, and yet, frankly, is way more interesting than Setsuna/Sara ever managed to be.
Lucifer/Alexiel is, hilariously, probably my favorite het coupling in a manga to date \o/ They're just awesomely abusive of each other and their story is both sad and fantastic. The ironic part being I have no real desire to see them GET TOGETHER, tho it would be nice if poor Lucifer could at least get LAID at some point, but the whole act of them trying to get together is fucking epic, and I'm going to recount it for you!
In volume... three I think? Setsuna (unknowingly) relates himself and Kira to the story of the two lovers who were cursed, one to take the form of a bird during the day, the other to take the form of a beast during the night, and so even though they could meet each other, they could never do so in their true forms. They could never speak, and never be together.
This is... actually very accurate, in it's own way. Take that story and stretch it out over ten thousand or so years and you basically have Lucifer/Alexiel. Only it's not quite that sad because it's too busy being badass.
The way it goes is once upon a time, Lucifer was dicking around in Heaven. Lucifer was, as Michael will tell you, Never A Nice Guy. He was emotionally manipulative from the get go, he would idly and deliberately hurt the people he knew admired him, including his own brother. He never... fixated on causing pain, I think, he would just do it the way you might stop to pick up a quarter on the street: The opportunity is there, so why not?
And since he did it so casually, most people didn't notice. Lucifer, or Lucifel as he was then, was the Morning Star, the most powerful angel evar, and surely the one destined to be the Prince of Light. He was charismatic... most likely due to his frank way of speaking, his cold beauty, his strength, and less because he tended to give inspired speeches. But either way, the heavens followed him, and only those hurt directly by Lucifer really came to realize his true personality. And... even those aware of it still tended to be trapped in awe of him.
Lucifer, honestly, found it all sort of funny.
Now... Lucifer knew his own nature. And while I doubt he made a HUGE EFFORT to hide it, he wasn't brandishing it around LOUDLY. But... he was BUSY. Angels were falling, and those that fell tended to become his. Kaori Yuki doesn't go IN DETAIL about any of this, but we do know that by the time he meets Alexiel, Lucifel is well down the path to becoming Lucifer. He's killed many angels, thousands infact, and 'soon his wings will turn black'.
So then, at some point, Lucifer gets SUMMONED BY GOD.
This summoning by God did not go well.
You see, when Michael and Lucifer were born, there was a prophecy that came with them. Basically that one would be the Prince of Light and the other the Prince of Darkness, and the Prince of Darkness would become the ruler of hell and fight god and etc etc. Because Lucifer was SO COOL and Michael was just a tiny angry midget who controlled fire, people tended to assume Michael was destined to betray them. Lucifer would have realized he was actually the one who would become the Prince of Darkness, and hell, he couldn't have had much of a problem with it because he sure as hell didn't fight it. But...
When he went to talk to God, God basically told him that Lucifer's very nature, his incredibly evil soul, his hatred for all his brethren, was how he was created and he had no choice in the matter. God created him this way only so that Lucifer could represent the 'bad' path to humanity. God gave humanity a choice, you see, and in this universe God is the Ultimate in what is Right, and so in order to let humanity choose God, there needed to be another option.
Kaori Yuki ONCE AGAIN doesn't really go into details on this, so it's never explained why when Lucifer was planning on being evil ALREADY he gets REALLY MAD when God tells him he's only doing exactly what he was created for. But... he does get REALLY MAD.
And I don't think simple anger covers it. The result of this conversation with God becomes Lucifer's Primary Goal for the next tens of thousand of years, and he never explains it, never justifies himself, never asks for help, never gives up, he sacrifices everything and everyone to achieve it without a second thought. He is a Very Driven Fellow.
Anyway, Kaori never explains it! But my guess? Despite himself, Lucifer really was just doing what he was created for. He just...angled it slightly differently. Instead of contenting himself with killing humans or angels, with attacking heaven and being the embodiment of evil, he decided to free himself. If God wanted a controlled world, he would bring about the opposite, a universe where people are not bound up in God's ridiculous cycle of what they are born for. And, through destroying God's 'big picture', he would no longer be bound to any fate or design himself.
NOT, understand, because Lucifer is really a cuddlebug at heart and was never given a chance to be a good guy, but because he wants to be who he is, evil or not, of his own free will. Not because he was created to be so. Really? He wants to be free.
SO!
That's where Lucifer was when he met Alexiel.
Alexiel meanwhile was trapped in Eden. God kept her there, her powers restrained, and told her she was a sinner for she'd eaten the Fruit of the Tree of Knowledge of Good and Evil (which just so happened to contain part of Alexiel's mother, and thus she was someone who ate angels, and thus a sinner!). God was basically a real dick! But that wasn't general knowledge at the time, and Lucifer, very angry over his recent chat with God, made a pit stop to rape the most beautiful angel God had ever created, who was kept in Eden and rumored to be an emotionless doll.
Things happen! Lucifer monologues and Alexiel does indeed act like a doll, not even acknowledging him he starts to molest her. Until she watches a bird die eating the fruit that had made her a 'sinner' and abruptly grabs Lucifer's sword, kills the dying bird and cuts out Lucifer's right eye =D
YOU CAN SEE THEY GET OFF TO A GREAT START \o/
In the Way of Shoujo Manga it's the look in her eyes that does it. Lucifer meets Alexiel, who admits she is trapped here in Eden by God, that she can do nothing for it, she was declared a 'sinner' for a sin she didn't even know existed. She had no other path in life, no choices, God had her backed into a corner and even if her prison was beautiful, it was still a prison. Which makes her, really, the only other angel Lucifer had ever met who realized their position. They were trapped by God, angry about it, unable to do a thing. They were not blessed or loved, but created as pawns for his amusement, and lacked a choice to the life they were born to.
So Lucifer decided he likes her a lot, kisses her, and then LEAVES.
Yes, yes he leaves. Nevermind that he COULD HAVE TRIED TO GET HER OUT. He is, afterall, the most powerful angel EVER. He takes off and tells her that when she escapes this prison she is his woman, and not to forget that, and then leaves. To... go be evil. Start a war against Heaven. Etc.
Later on, Alexiel points out that Lucifer always refused to help even those he loves, and this is hilariously true. Even Kira does it in his own way, and will sit around and read books while his friends get beat up until it starts going too far.
Anyway, the first war happens sometime after this meeting. And after the first war Lucifer and a helluva a lot of fallen angels go down to Hell. Only, Hell isn't inhabitable, so Lucifer sort of... makes the earth with his own body. Don't ask me how \o/ he's just really strong like that. But yeah, the ground of hell is Actually Alive. If you stab it it BLEEDS and that's because it's Lucifer's body.
He leaves that shell there for his people to live on, and gets another body, and goes up to Heaven again. He sneaks in, and by sneaks I mean probably slaughters a lot of people. This may or may not have been the Second War KAROI DOESN'T TELL US. Either way, he gets up to Eden again and this time asks Alexiel if she wants to leave, and she takes his hand.
As they are escaping Heaven, Lucifer is SOMEHOW trapped within a sword, no one ever details THAT either, since he's apparently never been defeated. My guess is God stepped in there. Either way, Lucifer's soul is captured within a Blood Crystal and imbedded in the hilt of a sword made out of Ether, the Fifth Element. It's name is Nanatsusaya.
Nanatsusaya drives a bunch of people crazy before he gets locked within a cave within Heaven, where eventually Alexiel comes back for him. She taunts him rather as if he didn't get captured rescuing her because they are awesome like that. Lucifer's memories have been sealed, and she tells him that if he acknowledges her as his master, one day when the war is over she will tell him his true identity.
Thus begin the awesome adventures of Alexiel and Nanatsusaya. Wherein A Lot Of Shit Dies.
Though Nanatsusaya lacks Lucifer's memories, including his memories of loving Alexiel, he still falls in love with her. She taunts him, of course, I MENTIONED IT WAS AN ABUSIVE RELATIONSHIP RIGHT? Right. But he falls in love with her anyway, and when Alexiel goes up to Heaven to kill her brother, the Inorganic Angel Rociel, she takes Nanatsusaya with her, because he's probably the only weapon in the universe that could kill Rociel.
EARLY canon mentions that Nanatsusaya dies, or breaks off, or something, in order for Alexiel to seal Rociel within the Earth. Again this is NEVER SHOWN TO US and it doesn't come up again, so I assume it got retconned.
Either way, Rociel's blood is spilled on Nanatsusaya which makes Lucifer's soul within the sword immortal. Alexiel, meanwhile, is captured and sentenced to an endless cycle of being reborn as a human, and cursed to be brutally killed in the early years of each life.
Nanatsusaya, still in love with her, follows her. He's a sword but a COOL SWORD and, now that he's unsealed, can basically move himself around in a spirit form. Nanatsusaya takes to finding Alexiel's reincarnation, and then locating a dying human. When he finds a dying human he tells them that if they allow him to use their body, he will do whatever they would have done had they been able to live.
Despite these deals, and the fact that he follows Alexiel hundreds of times, Nanatsusaya never really gets attached to the individual reincarnations. None-the-less, he watches her, protects her, but never really saves her. She always dies horribly: raped, murdered, cut up by a serial killer, hung as a witch. Whathaveyou.
One day though, Alexiel's newest form, a prostitute, tries to run away with her samurai boyfriend. They are caught, she is injured and he is killed, and Nanatsusaya talks to the dying samurai to ask for use of his body. The dying samurai's request? That he love Alexiel's reincarnation with his mouth, his hands, his body (have sex with her) and then free her, also with his own hands (kill her).
Nanatsusaya didn't get it... not because he didn't see how killing her would free her. He did. In every other life, Alexiel died painfully and horribly. If he were to kill her swiftly, with mercy, after having loved her, it would upset the curse placed upon her. But... Nayatsusaya didn't understand why someone who was dying would be worrying about another person anyway.
Still, he does it. Alexiel's soul recognizes him, calls him "the one I've been waiting for" and "the one who always watches me" or something to that effect. They have sex! Which is very possibly a first and last for them, and then he goes to kill her and she thanks him because no one had ever defied God for her sake.
Then she dies, and her next incarnation is Setsuna.
And that is basically EVERYTHING THAT HAPPENS BEFORE THE CANON EVEN FUCKING STARTS. Within the canon of timeline? Next time Kira sees Alexiel SHE TRIES TO KILL HIM, and this is after Kira lies to Setsuna and says he raped her in her past life. Then they FIGHT SOME MORE when Kira dies and Lucifer is reborn and Lucifer tries to kill Setsuna and she’s like “no, bitch, this is my perfect form >\” and lets not go into the part where Alexiel seems to think Lucifer is a HUGE FAILURE but at the end of anything embraces him anyway.
And at the end of everything, Lucifer could kill Katou, could kill Setsuna, could kill his brother and could betray everything but his own goals, but is also still waiting for Alexiel.
Who will, Setsuna is dead and she comes back to her own body, probably decide to throw a giant wrench in his plans to take over heaven JUST TO BE A BITCH.
\o/