Personally I loved the Keen-on-the-run story arc. As for what happened...
She was eventually captured by the authorities. The Cabal tried to kill her. Reddington kidnapped Peter (David Strathairn), the CIA director, and was going to give him to Venezuela to be charged with American war crimes. Reddington blackmailed Laurel, the National Security advisor, to exonerate Keen or the trial will commence and she'll be forced to answer to her higher-ups why she allowed the potentially embarrassing/damaging trial to happen. Keen was freed. Peter was killed from being thrown out of an airplane. The aftermath is Keen is free but can no longer be an agent. She is now an advisor for the Task Force, sort of as a liaison to Reddington to the team.
Pretty interesting. Is the show still going on? And thanks for your time