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It started, at least semi-consciously, at the Yule Ball. He watched her dance and talk with Krum and the seeds of jealousy took root in his soul. At least she was able to get an intelligent conversation from him, rather than her date.
“So Percy, I haven’t heard much about your work since the summer, but it seems you’re doing well if you’ve been promoted to making appearances for Mr Crouch at things such as this. How are you liking working with the Ministry?” He was flattered that such a radiant creature was paying him attention, and pleased when Krum seemed annoyed by their conversation and familiarity (he had been in her House and known her for three years after all). By the end of the night, deep in his soul, it had been decided that Hermione Granger was his other half and she shined like the sun. He just wasn't quite conscious of how aware he was of her. Yet.
He was on the outs with his family for standing up for his job, and now, nearly a year later, realizing he’d made a huge error in judgement in trusting the establishment over his own family, over her. Hermione had written to him personally after she’d found out from his family about their estrangement and begged him to reconsider his position. She’d insisted that although she hadn’t personally seen him, she trusted Harry that Voldemort was back.
Percy, of course, heard about the break-in of the Department of Mysteries when he’d come to work the next day, and that it was official, Voldemort was back. He should have trusted his family. Trusted his personal sun. He was appalled and terrified when he discovered through much digging that she had been nearly fatally wounded in the battle. He changed his allegiances then and there, but he was smarter than his family gave him credit. Once he really opened his eyes, he saw the Ministry had already been heavily infiltrated, and he was in a new position of not power, but access to knowledge. He couldn’t publicly disavow his loyalty to the establishment he’d previously supported without risking his life or those he cared about.
So instead of informing his family, who might not believe him, he sent one of twin charmed diaries to his personal sun and confessed his sins to her. She scolded him harshly, and he felt burnt under her rays, but at the same time she washed away the darkness that had clouded his conscience and absolved him. They communicated through her sixth year, then when the trio went on the run. He was her rock when things seemed overwhelming. He knew they planned to break into the Ministry but she refused to tell him details so that he could claim ignorance if they were caught. He hated the idea.
The day of their break-in he knew something was different. Occasionally the Minister would send him down with Dolores to the muggle-born trials, but today they ran into Mafalda Hopkirk at the lifts and Dolores was delighted to use her instead.
Percy felt oddly drawn to Mafalda, which was absurd because he held no sort of attraction to the woman, at all. As she left on the lift with Dolores, though, looking oddly nervous, he suddenly felt like he’d been hit with a Bludger. Hermione! She was using polyjuice, which meant his brother and Harry were around, too, so he made excuses to stay in the Atrium, knowing they were on a tight time limit. As they ran to the floo’s to escape and the grates came down nearly trapping them, Percy was able to take advantage of the chaos and stun some of their pursuers, unnoticed by all. He cursed when he saw Yaxley grab Hermione at the very last second, though. He was upset later when she wrote of what happened. His brother was injured - splinched - but his sun was safe, and on the run in the wilderness. He had never felt more relieved and lost at the same time.
Percy got word that there was going to be a battle at Hogwarts from Aberforth, so he Apparated to the Hogshead and rushed down the hidden passageway. His family was shocked to see him, but he only had eyes for Hermione. Her handwriting the last couple weeks had been very shaky and he suspected she’d been tortured but she never admitted it to him, not wanting him to worry. When he’d heard about the Gringotts break-in he’d nearly had a fit and had struggled to keep calm at work.
As he halfheartedly greeted his family he made eye contact with his sun. She grinned and raced towards him and he wrapped her in a tight embrace. “I’m so glad you came,” she gushed as he held her, breathing in her scent. She pulled away to look at him because he hadn’t said anything yet.
He was at a loss for words, but his eyes spoke volumes. Finally, he was able to get his mouth to work. “I love you, you’re my sun and I couldn’t possibly stay away. Please, when this is all over, can we talk?” Instead of answering him she pulled him in for a heated snog and they didn’t separate until Harry cleared his throat and reminded Hermione they needed to end this. His family just gaped at him, and Hermione was all grins as she rushed off with Harry to put an end to the battle between good and evil.