I believe that Penny is now the leader of an organization going against the likes of her father and his cronies. She uses his money to hire spies, infiltrate the orgainzation, spy on projects, things like that. (Kind of like Rachel Blake in the Lost Exp) penny knows her father made des make the wrong choices, so she is fighting back.
Penny has a network of people, trained military style, but more like spies. One of her top people, the parachutist, either volunteered or was chosen to go through the (**removed by author**) to the island, where the listening station guys located, and bring a message to Desmond. But what the heck do i know.