There was nothing romantic about the moment he realized he was in love with her. Unless you consider bifurcation romantic. Shinji didn't.
That moment when he saw it happen- saw Hiyori literally cut into two pieces- he felt something he had never quite felt before. There was anger and rage sure, but he was extremely familiar with those emotions. No, it was something else. The feeling that his heart was being ripped from his chest. A sudden knowledge that living without her was going to be some sort of torture he wasn't sure he could take.
He didn't even remember consciously calling out her name. It was so instinctual when it happened; a true cry from the heart. He grabbed her, cradled her in a way that she would have never allowed under other circumstances. She managed a pained smile and apologized to him for rushing forward, and that enraged him. She shouldn't be apologizing for something that should never had happened in the first place.
It was strange. He knew he'd be angry when he finally confronted Aizen. He had mentally prepared for that for a century. This though, this was something else. Looking down at her face, he felt a sense of primal rage like no other he had ever felt. There was also a sense of affection, affection for this girl who has exasperated and entertained him in equal turns for almost as long as he could remember. And strangely, he had a strong sense of regret. Regret that he hadn't said something sooner, tried to let her know that she was a welcome part of his life, flying shoes and all.
This was bad. Really bad. His brain went in a thousand directions at once, trying to find a way to fix it. He could the life bleeding out of her, and felt like part of himself was bleeding out with her. He called Hachi over, which wasn't fair to Hachi and his missing arm. Shinji didn't care though. Hachi could handle this. Hachi would have to handle this. There was no other option. He knew that Orihime could fix this, but that would require time. Time for Ichigo to go get her and bring her back.
Aizen mocked him. Said he liked what he saw. A light in Shinji's eyes he called it. Only it wasn't a light. It was a fire. A fire the likes of which Shinji had never felt before. He pulled her small body close one last time, then gently laid her down on the ground. Hachi would take care of her for now. She had to hang on. He couldn't let himself even consider the alternative.
So he put her out of his mind completely. It seemed cruel, but he couldn't afford any distractions. Not even her. He had to trust that Hachi would protect her.
Of course, he was soon dealing with injuries of his own. Aizen was even more formidable that they had considered. The hogyouku was something else entirely. In the end they won though. Well, Ichigo and Kisuke won really. Ichigo weakened Aizen for Kisuke's kidous to take effect. By then the 4th division had shown up. After having his own wounds taken care of, he went to search Hiyori out, scared at what he might find. He was relieved to see that Unohana herself was taking care of her. He planted himself by her side, a place he was about to become all too familiar with. Unohana assured them that physically Hiyori would be fine, but that she had to have the will to live. Then Unohana said something peculiar. She said that he was probably the one who would know whether or not Hiyori would have the ability to pull through. Better than anyone else. With that he knew. Knew that Unohana understood. That she could read it on his face. Every feeling, every worry, everything that was aging him faster than anything else ever had. Unohana watched his face, but he couldn't bring himself to look her in the eyes. She had always been a bit frightening. It didn't matter what he felt or didn't. It just matter that Hiyori lived.
Time seemed to crawl while she was unconscious. Shinji refused to leave her side. The other Visored tried to convince him to leave at first. They'd take care of her they told him. They soon learned that this was not negotiable. He was not leaving. So they decided to let him stay and took it upon themselves to take care of him as much as possible. He knew they probably suspected something at this point, but he didn't care. After a few days she began to stir slightly. She said something very quietly, and his heart lifted as he recognized his name. He told it was ok, she was ok. And then she said one word. "Baldy." He knew this was good sign. She was going to survive this.
She seemed surprised to see him when she was conscious enough to notice him there. She was still too weak to argue about it though, and he made sure she knew in no uncertain terms that his leaving was not an option. He saw a look in her eyes, a look of realization maybe. Whatever it was, she didn't try to argue anymore.
They settled into a new existence, one that saw them both softening. There was less arguing and name-calling and more actual conversations. Their shared history had not been for nothing, they actually got along quite well when they tried just a little. He put himself in charge of her physical therapy and training. It started with sitting, then standing, then walking. Their walks got longer, and they began to spend a lot more time alone. Away from all the others. He wanted to tell her, to say what it felt like when he thought he might lose her, but he couldn't quite manage the words. He knew she felt the same. He could see it in her face. For some reason though, neither one of them wanted to say it out loud. It was as if saying it might ruin the peaceful existence they had managed for themselves.
Then in the blink of an eye, everything changed. Soul Society wanted them back. He was offered his old captainship, leading the 5th. They were in bad shape. The young vice captain had been betrayed and torn apart. The division needed him, and it was hard to turn that down. Especially since it was partially his fault that they were in this position. And to be quite frank he owed them. They had saved Hiyori, and so he had to repay that favor. He thought she would understand if she gave him a chance to explain. He should have known he wouldn't get that chance.
Her reaction was even worse than he had imagined. To say she was upset would be a massive understatement. Everything they had built, every little tenuous connection they had made was soon frayed. The softness he had gotten a chance to see disappeared, replaced with anger and hurt. The anger he had expected in some ways, but not the pain of seeing her so hurt. It was unsettling.
There was a lot of yelling and name-calling. He just wanted to make her see, make her understand why he felt like he had to go back. So he told her he loved her. It was said almost in desperation. It had the opposite effect from what he wanted though. Instead of being pleased, she was even more furious. Furious that he would tell her that while getting ready to leave her. Because there was no way she was going back there. He wanted to grab her, shake her, anything to make her see.
So here they were. Back at the beginning. Except not exactly, because you can't take back what has already been said. For better or worse things had changed. So he decided to be patient. He left her with the assurance that he'd call her, and he did. She didn't answer at first, so he kept trying. Eventually she answered to yell at him for calling, but she didn't hang up immediately. Then one day the unthinkable happened. His phone rang. He looked down, saw her number, and smiled. It may not be where they had been, but it was a start.