Mentions episodes 1-4 of Book 3, but mostly takes place during "The Venom of the Red Lotus"
Author's Note: Some fans complained about the lack of Makorra in the Book 3 finale. This is my take on what Mako's thoughts may have been before, during, and after that battle.
Mako said he would always love Korra, because he knew it was true. What he felt for her was too deep to ever be completely erased. The only question was whether, and how, that love would translate into his actions.
He thought he should try keeping a distance for a while, because that's what his life would be like from now on, keeping a respectful distance away from her. He wouldn't avoid her when his police work and her peacekeeping efforts coincided, but he could turn down optional opportunities to be with her.
Mako tried to opt out of the trip to Ba Sing Se because, unlike their voyage to the South Pole, there were no high stakes. No lives were in danger; no evil was targeting Korra; and no one was immediately depending on any of them for anything. What was more, Mako himself was not essential to their mission of rebuilding the Air Nation. So he felt no moral obligation to go.
His attitude changed when they learned that Zaheer had escaped, and that Korra's life might be in danger as a result. Mako was just as devoted to protecting her as he had been before. It was only right, really: she was the Avatar, and he was a police officer. Protecting people of interest was part of his job. And protecting people he loved was part of his nature.
Mako hardly saw Korra during the final battle with the Red Lotus (if one could call it a battle—it was really a few separate, simultaneous fights). When he did finally see her, more dead than alive, he and Asami ran up to get a better look, but then they hung back, waiting to see what happened, whether she would live or die.
It wasn't that Mako felt any less concerned than he had at other times when he was seriously hurt. The difference was that this time, he wasn't needed. He didn't feel the same desperation he'd felt when he defended her against Amon or the dark spirits. The battle was over, and there was nothing he could do now to help her.
She didn't even need him close by—her father was holding her. Even if Mako and Korra had still been a couple, he wouldn't have had it in him to do what Bolin did, push aside his girlfriend's parent to get to her. It wouldn't have been right, when she was so close to death. Tonraq had known Korra longer and better than anyone else present. And that meant losing Korra would probably hurt him more than anyone else.
Mako had to remind himself, She's not yours to lose—at least no more than Bolin or Asami.
Even as he waited, even as Tonraq's face froze and Zaheer began to laugh, Mako tried to steel his heart against the possible blow. At the same time, though, he couldn't really believe that she was dying. She had already been through so much, and survived every time …
"You can still save her." Spirits bless Jinora. Mako had never felt more grateful for the airbender and her intellect, or for Su and her metalbending. The two of them together revived Korra. Mako could breathe again. Nothing had changed—at least, not in the sense he had feared.
Korra was still alive, that much was the same. Mako could be content with that. But everything about her was different. The poison left her physically debilitated, so much that simply walking tired her out. But she also seemed tired on another level, one that none of her friends or allies could quite identify, because she wouldn't—or perhaps couldn't—explain how she felt.
The last time anyone had treated Korra so fragilely was after Amon took her bending away. No one knew quite how to act around her, because on the one hand she had survived the battle and defeated the enemy, but on the other hand she was hurting.
Part of Mako wanted to help Korra; but again, it seemed like he wasn't needed for such a role. Her parents were staying with her now, and she also had Asami and the airbenders for company and support. Even though it used to make him feel awkward, Mako now felt glad for Korra and Asami's friendship. She could stay with Korra in her room and help her get dressed up for events without it being a big deal. No one judged them for being so close.
If Mako tried to talk to her, or offered to help her or do an activity with her, it would be awkward, and either she or others might misinterpret the intent behind his actions. Or it might make her miss how close they used to be. He didn't want to make her feel worse.
So he resumed keeping a respectful distance. He could be content knowing Korra was in good hands, even if they were not his own.
