Michael History
When God was experimenting in his attempt to recreate an angel like Adam Kadamon, he took the six wings and split them between twins. This not only spawned Rosiel and Alexiel, but also Michael and Lucifel. Only instead of giving them each three wings as he did with them, he gave Michael two and four to Lucifel. A prophecy was made about their birth; One would be the Angel of Light and the other would turn into the Angel of Darkness and fall. Lucifel was tall, strong and beautiful. Everyone loved him, everyone looked up to him as being perfect. Michael, who in a desperate attempt to catch up to his brother's power exhausted his ability to grow any further than a mere teen by maxing out his powers so young, who was always rash and short tempered, so much darker in appearance and personality than Lucifel, was thought to be the Child of Darkness. As such he was treated badly and shunned by the other angels, but he didn't care. The only one he wanted acknowledgement from was his brother, whom even he looked up to at the time despite his jealousy. There was one though, the woman that had raised him and his brother, that didn't treat him any differently. He saw her as a friend and someone he could actually trust as she actually believed in him.
Some time before the Great War Michael was already friends with Raphael, before the doctor became tainted and jaded. It was actually after Raphael's first sexual experience was forced upon him, and everyone in Heaven found out about it and shunned him, looked down on him for being a disgrace to Angels. Raphael had locked himself away, depressed and hating himself more than anything, when Michael quite literally bursted through his wall to check up on him and see what was going on. He tried talking to him and asking him what he was doing moping around so much. It's not certain if Michael was actually aware of what the rest of Heaven was saying about Raphael or if he was simply oblivious like always, but the fact that Michael viewed him no different and continued to treat him as he always had was enough for Raphael. Michael was his only true friend, and whether or not the red head was aware of it himself, he had somehow saved Raphael from dispair. Which explains Raphael's actions after the Great War.
Near the end of the war, Lucifer's rebellion against Heaven, Michael faced off against his brother in a fight. He was going to strike the final blow, but the woman who had raised them, the one he actually trusted, threw herself in the way. She chose Lucifer over Michael in the end. As the Demonic Army retreated, it was the look on Lucifer's face that broke Michael. Technically, the red head knew he had won the battle, he knew that he had finally bested his brother. But when he looked up at Lucifer, it was that same emotionless unreadable smirk looking down at him. His brother didn't acknowledge it at all. After the war ended, Michael secluded himself in his confusion and anger, the entire area around him engulfed in flames and heat so intense everyone was too afraid to get near him because they would get burned. Raphael, however, was the one to step forward. Michael had saved him, and he felt he should return the favor. He entered the area, ignoring the flames and ingoring his skin getting burned. He managed to talk sense into Michael, to tell him that he had to believe he won. Eventually, he managed to talk him into calming down.
Michael's first appearance in the manga is when he denies wanting anything to do with Sevi trying to recruit him to publicly appear for the sake of 'raising moral' when really Sevi was trying to gain supporters to go against Rosiel. Michael states that if Sevi wanted him to move or do anything else then he should bring him a war. After which he thinks over about the Messiah and how strong he is, going straight to Raphael's place to try and talk him into helping him out. He gets refused, obviously, as Raphael hates working with Michael for the fact that the red head is too temperamental and always messes things up which he then has to pick up after. Michael gets tired of hearing him talk and blows most of the place up in retaliation. Before Michael can get what he really wants, a fight with Raphael, his second in command knocks him unconcious and takes him back to the base so he won't cause anymore trouble.
It's short lived however as Raphael later learns that Michael had left to go to Earth in hopes of finding the Messiah and fighting him. He succeeds and badly injures Voice and almost gets beat after pissing off Setsuna, but Raphael shows up and when a distraction is given he grabs Michael and teleports them both away, much to the read head's bitching. Michael throws a fit and despite everything Raphael tries to tell him he hits him and declares rather childishly that they're no longer friends and he hates him before storming off. That, as well, is rather short lived as not too much longer later Michael shows up at Raphael's place and is brimming with joy and happiness after a good hunt, bringing Raphael a bunch of pointless gifts that he collected from the creatures he was killing to relax and calm himself down.
He doesn't even recognize Sara, who is actually in the body of one of the other Four Great Angels Gabrielle at the time, even when she snaps and starts yelling at him. Raphael manages to convince him to just head home but just as Raphy's predicted after about three steps Michael gets pissed off again as the fact that Sara stated she was the Messiah's sister finally sinks into his brain. From that point on, he is no longer on the side of the angels (not like he technically was in the first place) and instead is roped into helping out Setsuna and his group as not only does Raphael decide to help Sara but the other Great Elemental Angel, Uriel, also appears to assist Setsuna's group (luring Raphael and Michael into a trap to ressurect Setsuna's body).
Eventually though, Michael gets royally pissed off along the line because the entire time Raphael knew that Nanatsusaya, Setsuna/Alexiel's sword, housed the soul of his brother Lucifer. And that was the reason why Raphael pulled him away from the battle with Setsuna the first time around, because he 'couldn't win' and he probably didn't want Michael noticing or finding out about it and losing his cool completely.
Later on though, when Setsuna wakes up in Michael's chambers in a cage Michael explains to him the chaos going on. He tells him that the Seven Satans, knowing that Hell was collapsing around them as Lucifer's life was compromised by Rosiel, cut the lynchpins of Heaven and Earth, hurling Hell against Heaven. The top two layers of Hell and the bottom two layers of Heaven were smashed together and things could blow up at any moment. Michael then asks Setsuna about Kira and when Setsuna tells him that he's dead Michael loses his temper and gets pissed off, claiming that he was supposed to be the one to kill Lucifer himself. Michael then explains how in the final battle he was supposed to have won, but it didn't feel like he did. Setsuna calls him a coward and Michael tries to have him killed, but it doesn't work.
Nanatsusaya ended up saving Setsuna and tried to help him escape. Michael refuses to allow this and fights Setsuna one on one. However, Setsuna manages to pin him down and forces Michael to admit he hates Lucifer so much because he loves him, he can't bare the betrayal and feeling unloved. He then gets Michael to tell him where Sara's trial is being held. Michael not only tells him, but takes him there personally on his own ship.
After everything with the trial explods and settles down a bit, Raphael (who fell in love with Sara) locks her away and tries to kill Setsuna so he can have her himself. Michael gets in the way though and punches Raphael in theface, telling him to face the truth. They all go to Raphael's house, unknowning that Sara is now in danger because she was left alone.
With Rosiel controlling Lucifer and all Hell breaking lose (more than literally) the Seven Satans speak with the head Angelic forces and state that they'll give Setsuna Kurai (who was being kept in their possession by Hatter who was far too attached to the girl) in exchange for a non-interference pact. They weren't joining the Angelic forces, but they would simply let them do what they wanted without trying to stop them. Michael goes with Setsuna, Kurai, Kato and Uriel to follow after Rosiel. By the time everyone gets into Atziluth though, Uriel and Micheal become separated from Setsuna and Kurai.
When Lucifer stabs God, releasing Adam Kadamon who promptly robs Rosiel of his Crystal Heart, Uriel and Michael finally show up again to rejoin the others. After Rosiel allows himself to get absorbed into Setsuna they all go to the Angel birthing room to see the true body of Adam Kadamon, the real one. Which is where they learn that angels were born by consuming the flesh of their Mother, born committing the Original Sin. The real Adam Kadamon then tells them his consciousness is slipping, his power was split to create Alexiel and Rosiel. His body ripped apart and his head placed there to provide nourishment to the children but the Creator began a plan to reset the world. In order to stop Earth's time and seal God away they need to find the five elements and seal Adam's body so God couldn't abuse his powers any longer.
Michael can't sense Raphael's aura any longer, so Kurai volunteers to summon the wind and water dragons to make up for not having Raphael and Gabrielle there to help them. God sees what Uriel and Michael are doing and sends the embryos on them to stop them. Adam Kadamon uses the last of his strength to call the embryos away from the angels, to come to him. The angels are successful and the Tower crumbles.
In the end, Raphael falls into a coman due to his power being used up in saving Barbiel, the woman he realized he loved. Before he passes out, he tells Michael to be around as soon as he wakes up so they can finish their fight that was started when Michael punched him. Michael's last seen sitting there on the floor next to where Raphael is.