Reputation is a measure of your standing with the mission giving groups of Ascii Sector. The better your reputation, the more lucrative/interesting missions you are offered.
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Reputation window: low reputation with the Fixers, none at all with the others

Groups that are effected by your Reputation:

You can increase your reputation by successfully completing missions for the for the different factions. Failing missions decreases it. To see what your current reputation is activate your Quine 5000, go to Stats and then to Reputation.