The facts of this week's big case were these:
After the presumed suicide of her best friend at the nunnery, Olive went to Emerson for help to prove that Sister LaRue was murdered. Emerson, of course, showed up to help with Ned and Chuck, all disguised as priests and nuns.
After discovering some shady business at the convent - such as "schwag" from outside and some sort of lab set up in the bell tower from which LaRue supposedly jumped to her death - we learn that this nun was actually undercover. She was a scientist who was using the nunnery to perfect her perfect truffle recipe. Seriously! It's a long story, but at the end of the episode, all the suspects at the nunnery were off the hook. The reason?
Chuck determined that the culprit was actually Pigby, who simply wanted the truffles LaRue was hoarding. After this case was solved, Olive decided to go back home.
In personal news from the hour: Unable to keep the secret any longer, Olive told Ned - or made him guess, actually - that Lily was Chuck's mother.
This played into Chuck's main story line from the episode. She hired a family tree expert to dig into her past because she wanted to make the most of this second chance at life. But the guy came up empty and Chuck was left to cry over the fact that she had no past and no future, she was stuck.
Until Ned came to the rescue, that is.
He ended "Bad Habits" by telling Chuck the big secret about Lily being her mom and Chuck cried tears of happiness as a result. Now, she knew who she was.