Why do you think the Builders left instructions about how to escape the city of Ember?
There are a couple of main reasons for their leaving these instructions. The first reason is a practical one; the city is underground, and so the inhabitants of Ember have never lived above the ground. They simply have no idea about how the city was built, and so have no idea where it is, where it lies, or how to get from under to above the ground. It's therefore necessary for the Builders to give practical and geographical directions to those unfamiliar with the city's location.
The second reason has more to do with the predictable nature of power and of the people who have it. Although at first the mayors of Ember obeyed the instructions, inevitably a less trustworthy mayor came into power. Where former mayors had done whatever seemed best for the city, the current mayor, and most likely a couple of his predecessors, has only feathering his own nest in mind when taking office. The Builders most likely foresaw that there would be men like this mayor who would come to power and who would decimate the spirit and the purpose of Ember. They knew too that those good citizens of Ember would be threatened and would therefore need an escape route.
What could Lina and Doon have done differently to avoid becoming fugitives?
Lina and Doon are both very honest, upstanding citizens who believe that people should work together for the benefit of the city. They are disgusted by the actions of Loopy and the mayor and so report them because they believe the authorities to be upstanding citizens and honest leaders. This is an error in judgement; they are not sufficiently cynical as people to be able to deduce that the authorities are going to tell the mayor that they are the ones reporting him. To avoid being fugitives, they would have to be more worldly and therefore not assume that everyone is as anxious to weed out corruption as they are. They also would need to be more aware of politics, and of how a corrupt mayor is most likely to appoint corrupt officials to support him. They have a rose-colored view of human nature, which is laudable, but in order to avoid becoming fugitives they would definitely need to think their plans through more and consider what might happen if they are betrayed by those whom they trust in authority.
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