Lina is so excited at the thought of getting some colored pencils to draw with that she follows a rumor to Looper's shop. Seeing them in person is totally exciting: "Inside the box were at least a dozen colored pencils—red, green, blue, yellow, purple, orange. They had never even been sharpened; their ends were flat. They had erasers. Lina's heart gave a few fast beats" (5.33).
Seriously, girl, they're just a bunch of pencils. What's the big deal? Well, to Lina, the pencils represent the ability to draw the pictures she sees inside her head, especially her dreamed-of lit-up city. In that sense, pencils = freedom of expression, and so it's even better that they're pristine and not used up, like most of the stuff in Ember is. Lina can really put these pencils to work.
Sadly, the pencils become tainted because Lina ends up associating them with her neglect of Poppy leading up to the power outage. She's so entranced by the pencils that she loses track of her baby sister, who winds up in danger. And thanks to that little mishap, the pencils aren't all about joy and imagination and expression anymore. They're also about icky feelings, like guilt and selfish desire: "she took the two colored pencils from her pocket. They were not quite as beautiful as they had been. When she held them, she remembered the powerful wanting she had felt in that dusty store, and the feeling of it was mixed up with shame and fear and darkness" (5.80). It's a sad day when a kid's desire for art supplies becomes a symbol of shame and fear and darkness, but then again, there are a lot of sad days in Ember.
So when Clary compares the mayor's inner state to one of darkness, Lina totally gets what she's talking about: "Lina knew. She had felt it in Looper's shop as she hovered over the colored pencils" (13.9). It's a bummer that Lina doesn't have happy, carefree associations with the pencils anymore, but she also learned a valuable lesson about how greed can eat you up from the inside and make you act in not-nice ways that have huge consequences for the future. Now, if only the mayor had learned that same lesson.