Double Standards takes place during S1 E6 (F.Z.Z.T.).
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Ward lay in his bunk, staring up at the ceiling. His hands were laced behind his head, his door closed. He saw in his memory the look on Skye's face, the hurt in her eyes, as he'd fired off yet another shot reminding her of her treachery. Earlier in the day, he, Coulson, and Skye had stood around the holotable discussing the strange death of Adam Cross. Skye had run a detailed and comprehensive background check and analysis of Cross. When Skye said "He's clean.", Ward responded "Everybody looks clean on their first go around." and gave her a pointed look. Skye hadn't responded verbally but the wounded look in her eyes had spoken volumes. Afterwards, Coulson had asked Ward if he was being a little hard on Skye, and Ward had responded with a speech – filled with righteous indignation – about Skye's betrayal in lying to the team about her Rising Tide boyfriend.
He knew he'd pulled it off – been very convincing in his anger recently - but now, alone in his bunk, he couldn't help feeling a twinge of regret for how hard he'd been on Skye. It wasn't like he was a saint himself. "Damn," he thought, "I'm sitting in judgment when I'm worse than she is. I'm doing the exact same thing I'm so thoroughly condemning her for, except that I'm killing people in the process and she hasn't killed anyone." He frowned, then sighed, thinking "Maybe it wouldn't hurt to ease up a little on her. She's made a pretty good start at making up for what she did and seems to be trying hard to earn our trust. And she's not waffling and joking around about her training anymore, she's taking it seriously now and seems to be 100% dedicated to S.H.I.E.L.D. and to the team." He shrugged. "Who knows, starting to back off a little might strengthen the bond she feels, make her a better ally." He reasoned with himself that it was all about his mission, his need to ingratiate himself with his team – with Coulson's team, he reminded himself – and that it had nothing to do with Skye or any feelings he might have for her. "I mean, she's just a girl and a hacker, it's not like she really means anything to me personally." he rationalized. It wasn't like her smile made his days better, like her presence made the room a little brighter. And she definitely didn't make him feel more comfortable, safer, than anyone else had since… well, maybe ever. Because that would be weakness, and he wasn't weak, he was a double agent for Hydra, for Garrett.
As Ward closed his eyes to go to sleep, he sorted his thoughts and feelings into , compartmentalizing, and slowed his breathing. His last thoughts were of sparkling brown eyes filled with mischief and warmth, of long curly brown hair that smelled vaguely of flowers, and of a beautiful heart that saw the best in the world, the best in him.