In 2007, Clary and the others went looking for him at his New York apartment during a party he was hosting. At first, he said nothing about recognizing Clary, but eventually had to acknowledge the fact that he had known her since she was little, even commenting that he'd watched her grow up. At the party, he talked about his tragic past, and Alec Lightwood sympathized with him and tried to remove the morbid atmosphere, but Magnus brushed it off, claiming that it happened a long time ago. He openly flirted with Alec by asking him to call him and winking at him. Alec however, who had yet to 'come out of the closet', thought he was in love with Jace Wayland, his adopted brother. Magnus was later called upon by the Lightwoods to heal Alec, who had been fatally wounded while fighting the Greater Demon Abbadon. Isabelle said that when Magnus showed up he was quite in a rushed hurry to get Alec to a private room in order to heal him. After fully recovering, Alec confronted his and Magnus's growing attraction to each other and asked him out. Upon learning that Alec had never kissed anyone, Magnus kissed him (resulting in the couple's first kiss with each other) before arranging for a date with him within the week. Magnus and Alec had been secretly dating, even though Alec still thought he was in love with Jace. Alec refused to tell others about the relationship due to how homosexuality isn't approved among Shadowhunters, often resulting in them being kicked out. Magnus took Jace into his apartment when he was injured. The warlock was upset by this and nearly told Jace of his relationship with Alec, but decided against it, knowing that Alec wasn't ready for that kind of step yet.
Later, to prove her abilities, Clary "created" the Fearless rune, which Alec volunteered to have applied to his arm in order to test it to see if it works. When the rune took effect, he nearly openly told his parents about his homosexuality and his relationship with Magnus. However, before he could directly reveal who he was seeing and the importance of it, Magnus quickly used a spell to momentarily knock Alec unconscious and from revealing their relationship, knowing Alec wasn't ready for anyone to know about them yet.
During a fight against Valentine on his ship on the East River, Magnus was on a floating truck and managed to rescue Alec from drowning. Alec offered him what was left of his strength, as he was severely exhausted from using his warlock abilities, so he could continue to use his magic to help the Shadowhunters, who were still on board. Magnus hesitantly accepted his offer.
Eventually, Magnus ended up in Idris himself. While he was there, the city was attacked by demons controlled by Valentine, who was bent on wiping out all Downworlders and those associated with them. Magnus was fighting off a horde of Iblis demons when Alec showed up and saved his life. After this, Alec confronted Magnus about ignoring him. Magnus was angry with Alec because he still hadn't told his parents about their relationship and while he loved him, Alec assumed he was in love with Jace and wouldn't be with someone who loves him "the way [he] does." Shocked that Magnus had directly told him that he loved him, Alec made a deal with him; if they survived the battle, Alec would introduce Magnus to his whole family (including his parents) to which Magnus, while grinning in happiness, agreed.
A bit later, Alec passionately kissed Magnus in front of a huge crowd of Downworlders and Shadowhunters, including his parents and friends, finally revealing his sexuality and relationship with Magnus. Afterwards, true to his promise, Alec finally introduced Magnus to his parents.
Some time after the end of the Mortal War, Magnus and Alec were touring the world, with Alec occasionally texting Jace with pictures of them together. It seemed that they were having a reasonable time, as the photographs depicted Alec wearing his usual jeans, while Magnus wore themed outfits for the occasion. At one point, Jace asked Simon if he would like to see a picture of Magnus in Lederhosen, Berlin.
Their trip, however, was cut short when Camille Belcourt was being questioned, refusing to answer to anyone with the exception of Magnus, thus forcing him and Alec to return to New York.
Despite what can be assumed to be an excellent holiday, sparks begin to fly when Alec soon found out that Magnus had, indeed, dated Camille centuries before he was born. At this knowledge, Alec listened through the door while Camille and Magnus spoke, hearing her compare him to a man named Will. This further upset Alec, causing great tension between the couple.
Alec found himself finally confronting the fact about his mortality in his relationship with Magnus, and how he wants to live with Magnus forever. When he overheard Camille comment that "pretty boys" are always Magnus's undoing, he told the warlock that he felt trivial to him while also bringing up how he never did anything to be with his previous lovers forever in the past and that he felt that he's just another boyfriend in a long line to him, who would eventually die, as he goes on living. He further stated that it was especially unfair since Magnus was anything but trivial to him. Magnus tried to comfort Alec as he was dragged off to find Camille, who had escaped, saying that Alec was not trivial to him, but Alec was still left unconvinced.
Another issue among the couple was of Magnus not sharing his past with the Shadowhunter. In one scene, it was depicted that Alec angrily asked Magnus if there was "anything that he wasn't into" and questions if he slept with a specific werewolf. Magnus inquired if Alec would ask every person he had met such questions, if he's had a relationship with them, to which Alec only answered while still clearly upset, "Maybe."
After the final battle, and everyone was reunited, Magnus found Alec and they began to speak. Alec finally confided in Magnus of his fear of eventually aging, and not being with Magnus who would go on to live forever in his youth. He was particularly distressed that they might not even have a chance, and that Magnus had already seemed to have accepted his fate as a mortal. Magnus consoled his boyfriend, telling him that he wouldn't be any more ready to lose him in the future than he was "right now", which he firmly said was "not at all." Revealing he had truly fallen in love with Alec and wanted him forever. As a reconciliation, they were passionately kissing in a corner, wrapped up in each other.
Magnus confronted Isabelle about Alec, directly telling her that he loved Alec, telling her that he'd noticed and was worried since Alec wasn't "happy."
Magnus later also told Simon that if it weren't for Alec, he'd be long gone from the scene by then and would go into hiding until the battle and everything blew over.
Magnus got hurt while protecting Simon from Amatis, who had turned into a Dark Shadowhunter, receiving a severe wound on his chest. Alec let Magnus take his strength—like on the night of the battle on Valentine's ship—to heal himself.
Upon their return to New York, Magnus found out about Alec's private meetings with Camille. Alec ended up finding him in an abandoned subway where he was supposed to be meeting Camille, obviously waiting for him, much to his shock. Magnus was upset that Alec would consider taking his immortality away at all and kept it a secret, not bothering to tell him about Camille's offer. There he also revealed how he had, in fact, been considering taking away his immortality, revealing how that was part of the reason he wanted the Book of the White during the Mortal War. He said how since he had seen everything and been everywhere in the world, all he ever wanted was to simply live the rest of his life and grow old with someone he genuinely loved and wanted and hoped for it to be with Alec. Though Alec emotionally pleaded for another chance, Magnus refused, asking him to take his things from his apartment and to leave his key to it on the table, also saying he wished to never see him or his friends and family ever again, being tired of being their "pet warlock". The two shared one last passionate embrace and final kiss before Magnus reluctantly walked away, leaving a heartbroken and tearful Alec behind.For a quite some time after that, Alec kept calling Magnus but kept hanging up whenever Magnus picked up, and sometimes leaving him messages on his voicemail. This, eventually, resulted in Jace breaking Alec's phone in order to get him to stop. Magnus was just as miserable over his break up with Alec when Jace went to confront him. Jace bluntly pointed out that he was obviously unhappy, since his apartment was a mess and he had takeout containers everywhere, clearly gorging himself on take out food.
Later, Magnus went to the Hunter's Moon with Catarina for some drinks. Catarina brought up Alec, and told him she hadn't seen him so hung up on anyone like he was with Alec, adding that she saw him with Alec when they left for Idris in the Portal. She told him that with Alec, he was actually happy, rather than miserable, like when he was with Camille. Catarina realized just how in love with Alec Magnus was and brought up Tessa as an example that sometimes love is worth the pain of death. She then insisted that Magnus re-take her position as Council Representative for the Children of Lilith so he could go to Idris and make amends with Alec.
After deciding to finally open up more about his past to Alec, the couple reconciled and got back together.
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Malec is the most written ship in the Magnus Bane, Alec Lightwood, Shadowhunters (TV) and The Mortal Instruments tags on AO3.
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