You got Molly fired. That's quite rude. You're rude. Here's what happens in this plotline. If you don't want to fire her, you can check out the other Routes. Pansy.
Free Items
At some point, after the Protagonist has enslaved Molly, you can make her give you free items. Abusing it, however, causes her to eventually get fired after you enter the dungeon the next time.
The Protagonist can either cheer her up and say it's his/her fault, or scold Molly, saying she wasn't discreet enough.
Regardless of route, it causes Molly to blame herself for a while, while Derrick explains that there's nothing for her to blame herself for - he reassures Molly that his mother, the owner of the Item Shop, has no issue with money.
Molly, while crying, runs off and heads to the lake. There, the Protagonist cheers her up, causing her to wonder how the Protagonist knew where she was to begin with. The Protagonist remarks that it's a common brooding spot, saying that there's six other people brooding there at the moment.
The Protagonist then either tells her she's not at fault or that s/he'll take care of Molly, given how Molly is his/her slave. Molly, in either case, quietly accepts that she's too easy to push around.
Well Rested Molly
After Molly reaches level 12, the Protagonist runs into her in the streets once again. This time, she seems much happier and well rested. When the Protagonist remarks on this, she says she slept a bit more last night compared to normal.
Confused, the Protagonist asks how long she normally slept, so she said that after finishing the store and everything, she normally came home at around five.
The Protagonist remarks that it was a lot earlier than s/he thought, but Molly clarifies and says she means five in the morning. The Protagonist, shocked, asks when she sleeps and she admits to getting an hour or two of sleep before school starts.
The Protagonist remarks that Molly would be no good to him/her if she's dead from exhaustion, so she now needs the Protagonist's permission before doing any more work. Molly happily replies with "Yes, Sir/Ma'am".
At this point, Molly's Stamina skyrockets, giving her 4x as much Stamina as she previously had (for example, if she had 50 Stamina prior to talking to her, she now has 200). This also happens for her Stamina enchantment (the +5 instead becomes +20).
That's all that exists on this route as of version 0.60.