This sequence is really about a heist of a nasty virus called Chimera and its antidote, Bellerophon. Dr. Nekhorvich injects himself with Chimera and needs to go to Atlanta. He takes the antidote in his briefcase. He has 20 hours to reach his destination for “After you’ve been infected with Chimera, for 20 hours, nothing can save you. Not even Bellerophon.” His partner in the development ended up getting the virus and died just as they figured out the antidote. This happens before the film starts.
On the plane, he is sitting next to Ethan Hunt who he is calling Dmitry. The plane experiences “cabin pressure” problems and they tell the passengers to put on their oxygen masks. There must be something in the “oxygen” as all who put on their mask pass out. A team of bad guys, including the pilot don’t put on their masks and are unaffected. The pilot sets the plane on a course to crash into a mountain. “Dmitry” hits the doctor and stands up, pulls off a mask and is really the villain, Sean Ambrose. The team grabs the briefcase and parachutes out of the plane which then crashes into a mountain.
We’ve seen multiple movies with bad guys jumping out of planes, crashing planes, etc. This just follows the same formula, except this time you initially think it is Ethan Hunt on the plane.