Oh, frickity frack. Much to Sheldon’s dismay, Penny and Leonard (pretend) re-started their relationship because Penny didn’t want to admit to her father they’d already split. Leonard wanted a more impressive back story to their supposed reconciliation, but Penny made it clear: "Get over yourself. I whistled. You came running." And really, that seems pretty accurate to me. (Because she’s his lobster!)
Naturally, Penny’s father, Wyatt, adored Leonard mostly because he doesn’t have any babies, neck tattoos, or outstanding warrants. Penny and Leonard continued this ruse long enough that Sheldon had to amend the roommate agreement to account for all of Penny's "annoying personal habits." Eventually, they came clean to her dad. Wyatt made it clear he didn't want Leonard to give up on Penny. And all of Sheldon's work on the agreement was for naught.
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