The second version, used in the second half of season 3 and all of season 4, from "Mr. Monk and the Red Herring" (season 3) through "Mr. Monk Gets Jury Duty" (season 4). This version was introduced because Bitty Schram quit her role as Sharona Fleming and was replaced by Traylor Howard as Natalie Teeger, and therefore clips in the title sequence with Sharona would be outdated. This version was used in approximately 23 episodes, and replaced several season 1 and season 2 clips with clips from other season 2 and season 3 episodes.
The third and final version was used starting in season 5 with the episode "Mr. Monk and the Actor", and used all the way through the series finale. This version was used for approximately 64 episodes, and brought in clips from season 4 and season 5 episodes.
Randy Newman also wrote a new song for the final episode, "Mr. Monk and the End", entitled "When I'm Gone". The song won the 2010 Emmy Award for Outstanding Original Music and Lyrics.
The song has yet to be released on CD or to download.