Complex sentence: Penny and Sheldon start a quirky friendship (though she can still annoy him), Wil Wheaton begins appearing as Sheldon's arch-enemy, Howard begins to date Bernadette Rostenkowski, and, at the end of the season, Sheldon meets Amy Farrah Fowler.
Split into simpler sentences: Penny and Sheldon start a quirky friendship (though she can still annoy him). At the end of the season, Sheldon meets Amy Farrah Fowler.