In Apocalypse World, Michael and his fallen brother Lucifer's true vessels were never born, and thus when Lucifer rose from Hell and the Apocalypse began, Michael was forced to take another vessel. During this time, the humans thought the angels were sent to save them, but "one by one" the angels turned on humanity. Michael engaged Lucifer in battle - causing an EMP which fried all technology on the North American continent - and ultimately killed Lucifer by "[tearing] him apart in the skies over Abilene". Afterwards, Michael expected his father, God, to return and to give him answers about why he'd left. Instead, nothing happened. Thus Heaven and Hell remained locked in eternal conflict, and the Earth was devastated.
Michael subsequently decided to "be more God than God". As mentioned by Kevin Tran, Michael has the highest rank over the world and essentially serves as its God. Michael's campaign after Lucifer's death involved exterminating any and all humans deemed guilty of defying his regime - which involved authorising the angels to exterminate entire colonies of the human survivors, and rounding humans up for orderly extermination in angel-run POW camps. Michael himself would later admit that his intentions to do better than his father failed in his universe in spite of the Earth's ravaged state.
In The Rising Son, Michael shows up in front of Lucifer and Mary Winchester from the main reality after Lucifer effortlessly kills a group of angels who try to smite him and do not believe he is Lucifer. He can tell he's Lucifer, as the latter realizes he is the other world's Michael. Confused to see his brother, he questions how it is possible before he learns they are from another reality. Lucifer taunts him on not being like his counterpart and Michael tells them of his Lucifer's fate and shows he desires to do the same to this Lucifer, who responds by punching him. They fight before Michael quickly defeats and restrains Lucifer.
Michael decides to spare Lucifer for an unspecified purpose, saying he "needs him".
In War of the Worlds, he imprisons Lucifer and Mary. He has Lucifer placed in a cage and looks through his mind to look upon the world he came from. Seeing a chance at a better world, Michael decides to invade it and has Kevin Tran make a portal to enter the world. Michael taunts Lucifer over his powerless state, as the latter defends himself. Michael asks Kevin what he needs for the spell as the latter states the spell he's creating needs the essence of an archangel.
Not wanting to waste his own grace on it, Michael steals some of Lucifer's grace but leaves enough for future use and heals his wound. Kevin then does the spell, which is successful in opening a rift but Lucifer uses it as a chance to break free and jumps through it, returning to his world. Michael angrily tells an excited Kevin to fix this problem as he expresses fury at Lucifer's escape.
Following Lucifer's escape to the main reality, he rescues Castiel from hostile angels and warns him of the threat that Michael poses, something he feels warrants them working together, despite their past differences. Following their capture by Asmodeus, who also becomes aware of the threat from this Michael, stating if it was true he needed Jack to help him out.
During Various & Sundry Villains, while held captive Lucifer mentions Michael as Castiel remains skeptical of these claims. Lucifer soon compares this Michael to his own brother as he stated that when he puts his mind to something he'll do it. Lucifer tells Castiel there will be little time for Michael to arrive. He soon reveals Michael is torturing Mary Winchester, which horrifies and angers Castiel who cuts him off.
After escaping Asmodeus, Castiel returns to the bunker and reveals to the Winchesters that Michael intends to invade and take over their world, which worries them. The brothers intended to use an angel tablet that Donatello Redfield could read to use a spell and open a rift to get their mother and Jack out of the world before Michael harms them. Asmodeus (while disguising himself as Castiel) talks with the prophet for information on Michael and receives a little.
After Lucifer escaped the Winchesters and Castiel, Arthur Ketch also offers to act as double agent for them since he knew of both Lucifer and Michael's threat.
Asmodeus later states he can't risk the threat of two archangels (Lucifer and Michael) giving him trouble. To have a contingency plan for Michael's possible arrival, Asmodeus reveals to Ketch that he had an Archangel Blade and Gabriel in his possession.
During Good Intentions, Michael watches impatiently as Zachariah uses mind manipulation on Jack to coerce him into forming a rift to his world. Zachariah assures Michael his methods will work. However, Jack wakes up from the illusion and identifies Michael who flings both Jack and Zachariah aside and prepared to make the Nephilim submit.
Michael easily overpowered Jack and threw him in Mary Winchester's cell. When Jack awoke, Mary told him of Michael's intentions to kill her in front of Jack if he refuses to comply with opening a rift to their world so Michael's army can invade. The two prisoners later escape, due to the weakening of warding in Michael's fortress. Infuriated by their escape, Michael dispatches Zachariah and a squad of angels to pursue them but warns his subordinates not to fail him.
In the end, Zachariah is killed along with his squad by Jack who is praised for saving the human colony but he tells the humans for them to be truly safe in this world is that he has to kill Michael and free the world from his grasp.
In Bring 'em Back Alive, it is mentioned a human resistance led by Jack and Mary has formed against Michael and his army. An angel commander wanted to bring Charlie Bradbury before Michael since she stood in the inner circle.
In the main universe, Gabriel is informed of this Michael's impending invasion and did not want to fight him.
During Funeralia, Castiel went to Heaven to seek out the angels' help in fighting the alternate Michael who wants to invade and conquer their world. The angels were shocked to hear this though wary of him, they decide to hear Castiel out. Naomi also promised to help Castiel in the problem with Michael if he locates Gabriel for Heaven.
In Exodus, as Sam and Dean were convincing Jack and Mary to evacuate to their world both insisted on staying to defeat Michael. The brothers got through to their mother while Lucifer told Jack not to make a rash decision as it might cost him so much.
As Sam, Dean, Gabriel, and Lucifer were evacuating the humans from Apocalypse World through the rift, Michael made his entrance by killing many humans in his arrival. He greeted his foes as his appearance shocked the Winchesters and company at finally seeing him in person. Lucifer stepped forward to attack him as Michael mocked Lucifer by sarcastically asking if he really wants to fight again after their recent altercation, which Lucifer simply responds by agreeing and throws a blast at Michael. Michael is barely knocked back, however, and soon blasts Lucifer, swiftly knocking him down. He then approached the Winchesters and was surprised as he saw the alternate reality counterpart of his Gabriel.
Gabriel told Sam and Dean to retreat as he engaged Michael who readied an archangel blade, the two fought and although Gabriel briefly held his own, Michael quickly beat Gabriel and killed him. Michael tried to go after the Winchesters as they retreated but to no avail. He then turned his sights on the weakened Lucifer who was left behind by Sam.
Afterwards, Michael was seen talking with Lucifer as they were making a deal to get to the other world. He was skeptical of Lucifer's trustworthiness but the latter told Michael of the ingredients for the ritual as he asked what he wanted. Lucifer wanted his son while Michael wanted everything else and questioned if they had a deal.
In Let the Good Times Roll, Michael suddenly appears in a gas station to the shock of the Winchesters and Castiel. Unable to defeat Michael, Dean ignites a trail of holy fire, holding Michael back long enough for the Winchesters and Castiel to escape in the Impala.
Shortly afterwards, Michael breaks into the Men of Letters bunker, causing the Winchesters to order their mother and Bobby Singer to flee. Michael attacks the Winchesters and Castiel who prove to be no match for him. Strangling Dean slowly to death, Michael gloats about his plan to cleanse the Main Universe before Sam's prayers draw Jack to the bunker. Jack blasts Michael away from Dean with telekinesis and causes Michael to suffer great pain and bleed from his eyes and ears. Before Jack can kill Michael, Lucifer appears, angering Michael that Lucifer has betrayed their deal. Too weak to do anything, Michael watches the confrontation between Lucifer and Jack, ending with Lucifer stealing Jack's grace and disappearing with Jack and Sam.
With Lucifer gone, Dean and Castiel turn on Michael who, severely weakened, explains that Lucifer won. Michael explains that having consumed a Nephilim's grace, Lucifer is "super-charged" and can now end the whole universe if he wishes. Michael admits that he no longer possesses the strength to defeat Lucifer in his current state with a "banged-up" vessel and appears to accept that they are facing the end of everything. Dean remembers that he is the Michael Sword, Michael's perfect vessel who will make Michael stronger than he has ever been. Michael admits that together, he and Dean have a chance against Lucifer and seeing no other choice, Dean offers Michael a one-time deal: Dean remains in control while Michael powers him so that together they can fight Lucifer. Michael accepts the deal and Dean becomes his vessel.
As Jack is about to commit suicide to give Sam a chance to live, Dean appears in the church with Lucifer, Sam and Jack. With Michael now powering Dean who remains in control, Dean battles Lucifer, using several of Michael's powers in battle. Finally, thanks to having Michael inside of him, Dean is able to kill Lucifer with Michael's archangel blade.
Shortly after Lucifer's death, Michael goes back on his deal with Dean and takes full control of Dean's body. Thanking Dean for "the suit," Michael teleports away with Dean's body and later walks down a street wearing an old-fashioned suit and a British flat-cap as his new outfit.
In Stranger in a Strange Land, in the weeks that passed, Michael wanders the Earth asking others what they want but he is often disappointed in their answers even hurting them for their responses such as Jamil Hamed. Michael comes across Anael who is shocked to see him in Dean's body. After shrugging off her questions on why Dean gave his consent, he asks about her desire and ignores her statement of possessions before he comments that she wants love and acceptance, he labels her want as human and pathetic. He states that he knows that there few angels left and thought he could help but if they are like her, then they are not worth saving either before he leaves her. At one point, he came across the demon Kipling and their talk led the demon wondering about his own desire. Eventually, he seems to have finally found someone to answer his question truly honestly and a species that seems worth saving - monsters and states that they should work well together.
In Gods and Monsters, Michael is shown experimenting on captured vampires, mixing his angelic grace with their own blood and then feeding the vampires it, but this results in their deaths. A few escape and attack him but he kills them though allows one Lydia Crawford to escape in order to use her as a bait for a trap. While looking in a mirror, he is surprised when Dean manifests and demands that Michael leaves his body, only for Michael to refuse and bluntly state that he owned him and cancel Dean out.
Later on, Michael lures a female werewolf Melanie into his room and overpowers her after she tries to attack him. He forces her to summon her pack leader Philippe and reveals his archangel status to them before negotiating a deal with the leader with the intent of improving the monster race as he views the monster race as pure since they only kill for survival. He also assures Philippe that angels nor demons would be hindrance to his plans of wiping out humanity and he has found a way to help overcome their weaknesses.
Michael appeared before Lydia and told her why he spared her by revealing she was just the bait for a trap he set for Sam, Mary, and Bobby. Much later for unknown reasons, Michael leaves Dean's body and his whereabouts are unknown.
During The Scar, it is revealed that before Michael left Dean's body, he sought after Alternate Kaia and assured her that he wasn't Dean after she expressed hostility. Michael offered to form an alliance, but she refused and attacked him instead. Although the Archangel defeated Kaia and tossed her aside she managed to use Michael's arrogant mistake of not immediately dispatching her to trip him, regain her spear and wounded him in the arm before escaping. The wound is still visible in form of a scar that prominently stands out on Dean's skin.
It was mentioned in Nightmare Logic, that he has planted dozens of his enhanced monsters in quiet places so as to draw out hunters and kill them. One monster confused Dean for Michael until the latter informed him this was not the case but told Dean there were several monsters around. After killing the monster, Dean and Sam spread the word to other hunters of Michael's plans and his monsters so they will be better prepared.
In Byzantium, the angels have kept tabs on him and have suspected his whereabouts. Naomi offers Michael's location as a reward for his sacrifice in saving Heaven from The Shadow. After Jack's resurrection, Team Free Will think of a plan to defeat him now they know where he is.
In The Spear, Michael is seen in a new vessel and has his forces take over a building in Kanas City. With Melanie's help, he meets new recruits and takes note of Garth Fitzgerald IV and points him out as Dean's friend after remembering his face from possessing Dean. Michael is not sure of Garth's trustworthiness but stops after the latter assures him since he has to preserve his family's safety. After Garth and fellow recruit were given grace by Melanie to improve themselves, Michael has Melanie dispatch a few monsters to go after Alternate Kaia and her spear. Michael later approaches Garth and tells him they need to talk, to his worry.
Much later, he appears at the Kansas city post office where he intercepts Sam and Jack. Michael has one of his werewolves take Jack away while revealing to Sam of how he holds the hyperbolic pulse generator, which he soon destroys to foil a plot to defeat him. After overpowering the hunter, he leaves him unconscious and mockingly wishes him a good holiday.
In his office, Michael talks to a captive Jack and offers him a position in his army. Michael tells Jack that they are family with their powers and can make the world theirs if they sided together. Jack is not fazed and denounces him as a monster as Michael tells him that he'll watch everything die before he leaves. He later sits impatiently awaiting his enemies' arrival before he senses Castiel and confronts him. Michael effortlessly overcomes the latter's attempts to attack him and drags the wounded angel to his office where he is met by Sam and Dean who armed with Spear. Michael fights Sam and Dean, knocking aside Sam and fighting Dean while stating everything happening is on him. However, Dean manages to regain footing and holds his ground even landing decisive blows on Michael's vessel before he holds the spear at his head. Dean readies to kill Michael but has dizzy spells before Michael's vessel falls dead or unconscious and Dean breaks the spear, before it is revealed Michael took control of him again.Michael explains when first having Dean as a vessel, the latter resisted in accepting it and he decided to leave him but "left the door open a crack" in his mind so that he could return at will. Michael tells Castiel that he waited to break Dean's spirit and has now locked him away to prevent his interference. He taunts Team Free Will by telling them, nothing stands in his way now and his monsters are on the prowl awaiting his signal, which he soon gives with a snap of his fingers.
In Nihilism, after snapping his fingers, Michael changes to his traditional wardrobe. Michael tortures Team Free Will as he reveals that he will destroy everything, but his gloating allows Sam to distract him and Castiel to place Supernatural Handcuffs on him. Michael is undaunted as his monsters start pounding on the door, forcing Sam to call for a Reaper to appear. While Jack and Castiel can't see the reaper Violet, Michael notices her presence and taunts her about locking Death away and the enslavement of her kind in his world while she is disturbed by this and taunts his situation. Soon, Violet gets orders and the group are transported to the bunker.
Michael continues to taunt the group about his situation and Dean is under his control. Soon he insults Jack by telling him how Dean felt about his birth before Castiel steps in to have Jack leave. Castiel asks Michael how he could try to destroy a world, as Michael reveals that in his fight with his world's Lucifer, he realized that God would never return. He continues from seeing God in Dean's memories, as well as spending time in the Main Universe, he deduced why God never returned. He concluded that all of the realities in the Multiverse are failed drafts and God kept on creating new realities with different scenarios in an attempt to create a perfect reality. This causes him to gain the determination to destroy the multiverse and even attempt to destroy his creator. When its revealed Michael is stalling for his monsters, the group decide to come up with a way to eject him from Dean. Using Mind-link device, Sam and Castiel resolve to enter Dean's mind and get him to eject Michael who invites them to try but swears to crush them.
It is revealed Michael locked Dean in an imaginary bar with Pamela Barnes and a loop of the same event to occupy him. Soon Castiel and Sam get through to Dean who realizes the situation, just as Michael appears (in form of Dean). The group realize he is powerless in Dean's mind and attack. Michael fights the trio and gains the upper-hand over them before mocking them on trying to get him to evacuate Dean's body since it might cause physical repercussions on Dean. Hearing this, Dean decides to not eject him but keep him locked away. With help from the others, Dean puts Michael behind a locked door while he regains control of himself. Because of his imprisonment, Michael's monster army are left in disarray and scatter, stopping the threat. In Dean's subconscious, Michael continuously bashes on the locked door and screams to be released as Dean struggles to keep him trapped but worries over his control. Billie appears to Dean and notes on the archangel bashing around in Dean's mind are keeping him occupied though warns Dean that Michael most likely won't stay trapped for long. According to all but one version of Dean's fate, Michael will escape from his prison and use Dean's body to destroy the world. Billie gives Dean the book revealing the one path that defeats Michael and protects the world from him.
During Damaged Goods, Michael is fighting hard to get out, while it is revealed Dean intends to trap himself and Michael in a Ma'lak Box and sink it to the bottom of the ocean which is what Billie revealed to him is the only way to stop Michael from using Dean to destroy the world. Dean is talked out of the plan by Sam in Prophet and Loss, keeping it as a last resort and Michael is still trying to break out.
In Lebanon, Dean attempts to use the Baozhu to get rid of Michael for good, believing it to be his deepest desire. Instead, the wish brings John Winchester from 2003, creating an alternate timeline. The Winchesters are forced to destroy the Baozhu to send John back to his own time and set things right.
In Ouroboros Michael continues to try to break free from Dean's mind with Dean telling Castiel that its taking all of his concentration to keep Michael contained. As a result, Dean is barely even sleeping anymore.
After Dean is knocked unconscious by the gorgon Noah Ophis, he loses concentration and Michael is able to escape his mind. However, rather than take control of Dean again, Michael abandons his body and visits Rowena in Dean's form, seeking her as an alternate vessel. Michael threatens her but she is not fazed, as she reveals Death informed her that only Sam could kill her permanently. Ultimately, Michael is able to get Rowena's consent by threatening to come back in a different vessel and slaughtering everyone in the Bunker that Rowena cares about and forcing her to watch. In Rowena's body, Michael slaughters several hunters and smites Maggie before gloating to the Winchesters, Castiel and Jack.
As Michael inflicts multiple ailments upon them, Jack taps into the power of his soul and battles with Michael who taunts Jack. Jack is able to withstand Michael's attacks and exorcises Michael from Rowena. As Michael swirls above everyone in a cloud of white light, Jack raises his arms and declares that the archangel won't hurt anyone ever again. Jack then incinerates the archangel away before consuming his grace. Jack announces that Michael is dead and reveals that Michael's grace has fully restored Jack's own powers as a Nephilim.
In Game Night, Castiel informed Anael of Michael's death and she remarked "good night sweet prince".
During Moriah, Sam mentions Michael when he asked God about the alternate realities, God admits that he found the alternate universes to be boring but appeared to be shocked when Sam asked him if what Michael said is true. God also told Sam not to take what the alternate Michael said to heart and called the latter crazy.
In Our Father, Who Aren't in Heaven, Castiel shows the Main Universe Michael several of his memories as proof of God's betrayal. These included some of his memories of the alternate Michael when he was terrorizing Earth. This helps to convince the Main Universe Michael who is particularly shocked to learn that he isn't the only Michael in existence.