After he got out of Raccoon City, the government thought he knew too much. At the same time, surviving the outbreak proved he was very capable at dealing with BOWs, so they decided to recruit him to work with them. They blackmailed him, by threatening Sherry.
Leon accepted to work for the government. He was trained and became an agent, specialized in dealing with situations involving BOWs. He was sent in a mission in 2002 to capture a BOW dealer, alongside Jack Krauser (Darkside Chronicles: Operation Javier scenario).
Later, he became involved in the presidential security, and that's why he was sent to save the president's daughter in 2004 (RE4)