I saw it in the theatre. I have the 2009 blu-ray release. A t least 3 scenes are not on the blu-ray or were changed and the blu-ray has no "Deleted Scenes" section. It changed the ending of the movie. The first scene was the "We'll clean their chronometers" line. I thought it was funny but I think many fans though this line was dumb. The second scene, I think, was the mind meld between Spock and the female vulcan. I think she mentioned Colonel West (Rene Auberjonois) as one of the conspirators. The third scene is near the end. McCoy pulls off West's klingon mask, revealing him as the assassin. These are the scenes I remember seeing in the theatre that are not on the blu-ray. I guess Paramount decided it didn't like the scenes so they were removed for the blu-ray release but why not have them as deleted scenes on the blu-ray? Did Paramount think the scenes were so horrible - was Paramount so embarrassed - that they wanted to pretend that the scenes never existed? Star Trek has always used navy ranks and "Colonel" is army so "Colonel West" doesn't make sense in the Star Trek universe so that might be the reason for removing the scenes but it doesn't explain why they weren't included as deleted scenes.