The ending of Mission Impossible 3 settles three things at once: Davian is dead, Musgrave is exposed and shot, and Ethan survives the explosive in his head. Ethan kills Davian by throwing him in front of a truck, and the improvised shock from his makeshift defibrillator stops the device from killing him. Julia, who seemed to have been shot, then kills Musgrave and revives Ethan, and the couple leave on their honeymoon with Ethan back on good terms with the agency.
In my opinion, the choice that matters most is what the film does with Julia. She ends up as an ally who knows what Ethan does for a living, and it could be argued that this keeps him from being a lone operator: the closing image is a honeymoon for two, not another solo exit. The film also plants that idea early, because the first act is built around a woman who believes her fiance has a desk job, so the payoff is the reveal she earns by surviving Davian's kidnapping.
Musgrave's betrayal is the other piece worth reading closely. A traitor inside the IMF echoes the mole story of mission impossible 1996, where Ethan sets out to clear his name and find the real mole, but this time the traitor is a senior figure who helps Ethan escape custody before turning out to work with Davian. That structure matters in the Shanghai stretch: Ethan steals the Rabbit's Foot believing he has an ally on the inside, and the reveal rewrites that whole sequence.
The finish is also quieter than the film around it. Davian's death comes at street level, with a truck and a thrown body, rather than as a large effects spectacle like the ILM built Shanghai or the Vatican raid. That being said, the ending is not the last word on Julia, since Monaghan returns in the role in mission impossible fallout.