Quite a bit of narration for a while... If guys could bear with that would be great. If not... Sorry.
Something was off and, despite all of his genius, Sheldon just couldn't understand what. He had been missing Leonard terribly, and Amy was hardly around, causing him to miss her too but now...
It made no sense. Everyone was back where they should be, back in Pasadena, in his life and his routine but suddenly he found himself longing for the times when they weren't. When it was just him, Penny and a 'Supernatural' marathon. Not that he liked that hokum, he watched it for her... If he happened to get a little engrossed, it was only because he was bored and wanted to watch a cult-series with his best friend.
The thought of Penny being his best friend confounded him; Leonard had always had that title. Leonard drove him around, and played games with him and... Betrayed him. Countless times now really.
The time where he almost destroyed Sheldon's career came to mind, and when he carried on relationships with women that he made it clear that he didn't approve of. And of course, that time he slept with Sheldon's friend Elizabeth so soon after the termination of his and Penny's, admittedly, predeterminedly-catastrophic coupling. He fleetingly recalled the look on Penny's face, which was forever etched into his memory, thanks to his eidetic memory, causing a sudden wave of fury wash over him and the pencil in his hand snapped and splinted.
A small 'oh dear.' was muttered before Sheldon began cleaning his mess, thoughts again wandering to the confusing feeling of wanting Amy to leave, but not leave; he wanted her there, yes. But it felt that he was getting less romantically attracted to her everyday and he often felt as if he was spending time with an intellectually-increased version of Missy; how he longed for the days when it was just him and Penny again. Sleeping in her bed because he felt lonely and missed Leonard, her creeping in and sliding under the covers in her sleep...
Sheldon, who had been collecting the shards from his pencil from the floor, let his hand fall lax as he bolted suddenly upright, the shards finding their way to the carpet once more. 'Dear lord! Please, for once, let me be wrong!' he blurted, ignorant to Penny and Leonard's arrival, who shared confused yet bemused looks, before Leonard shook it off and started talking about... Something extremely dull that Penny took no notice of. Her thoughts, unwittingly following those of Sheldon before her.
Of course, unlike her socially-awkward friend, it took less than a minute for Penny to make sense of them and as she did, she felt the colour drain from her face which Leonard obviously noticed because he pulled his head out of his arse long enough to ask 'Hey, you ok?' and at the shake of her head signalling no, it was Leonard's turn to catch on? 'You're breaking up with me again, aren't you?'
Three bottle of wine and two vodka shots later, Penny still had no idea what to do about the fact that she was in love with Sheldon. After much, much consideration, (and booze), She narrowed the actual problems with this down to three main reasons.
1) Amy and Leonard 2) His apparent disinterest in adult relationship. A.K.A sex. And 3) Sheldon doesn't like her back.
Three days pass and the weight she's been carrying in this time lessens slightly when Amy tells her that Sheldon has terminated their contract and that, as a result, she will be completing her marital contract will prince Faisal sooner than anticipated. A further month and she can't help but notice the distinct lack of emo music form apartment 4A and more weight lifts at the discovery that Leonard has moved on and is now in a relationship with Sheldon't now former assistant, Alex.
Points 2 and 3 aren't trivial little things that will go away though. Her and Sheldon, as results of their breakupa have been spending more time together, and touching more and however innocently, it is drastic progress for Sheldon, who can now touch hski with immediately running for his purel. His argument is that 'he has become acclimatised to her personal germs' but Penny can't help but notice that he still sanitises frantically when in physical contact with the others.
Regardless, Penny knows that life isn't a fairytail, especially not when Sheldon Cooper is involved, so they maintain their friendship, both hyperaware of any paradigm shifts, no matter how gradual and minuscule they may be.
It isn't until a trip to the zoo that anything changes and this is six months after they had both become single. They were standing at the koala enclosure when Penny caught sight of his special grin, reserved for these animals. In turn, a lighthearted smile graced her lips and she watched him out of the corner of her eye which did not go unnoticed by the tall physicist who had, unbelievably been becoming more, and more frustrated that this self-proclaimed big ol' five had yet to make a move when he had observed that she too reciprocated his amorous feelings, if not at the very least some sexual attraction towards him. At a later date he would blame, but not resent this frustration for prompting him into performing his next action; the action where he whirled Penny round to face him before bending down and pressing his lips against Penny's; and as her arms came up around his neck he couldn't help but be grateful that they had waited till now - he couldn't think of a more romantic setting than by the koalas and when they were separated he was grateful that Penny couldn't tell he was wearing his koala smile, even though the elevated heartbeat and dilated pupils where definitely nothing to do with the adorable animal.