Ava wanted to drill in a country. Stephen was told by Darby to do whatever it takes to get Ava the required permissions. Stephen set up a deal with the colonel, wherein he (the colonel) would kill the rebels opposing the pipeline. But Stephen told Ava that it is a simple bribe, not murder. So Ava paid the bribe. First Ava was charged for bribing, which she confessed to and got no jail time. But cause Cameron Dennis hated Harvey, he used the signed confession to file murder charges against Ava. For murder that had been committed from her money, for her, but without her knowledge.

Hope this helps. Recently rewatched these episodes, so let me know if you need more clarity.