Rating: PG-13 to be safe
Disclaimer: Sherlock Holmes and Watson belong to Arthur Conan Doyle, events from the movie belong to Guy Ritchie.
Summary: Watson's possible underlying motives during the movie.
Watson may not be at Holmes' level of observation and deduction, but some of his observations were disturbing to himself. As a military man he was used to order and regimentation, but a small part of him enjoyed the chaos of being with Holmes. He loved Mary, but part of him loved Holmes too. He didn't plan to say it, because of law and the possible consequences to both of them. He planned to marry Mary because he loved her, and also get away from the temptation of Holmes. That had been the plan, but it wasn't working as well as he thought it would.
The feel of Holmes' head against his back was brining back memories of other times he slept on him, which made leaving difficult. He called himself mentally disturbed and listed things that irritated him about Holmes, but that alone wasn't powerful enough to break Holmes' hold on him. When he said he understood, the look in his eyes let Watson know that he understood what was unspoken.
Holmes was resisting him leaving, and a part of Watson himself was resisting leaving. He blamed that part every time he went to find Holmes after he found the revolver left behind. He also blamed that part every time he went with Holmes instead of going to meet Mary. He also held that part responsible for calling Holmes "gorgeous" the first time he saw him after the factory explosion. He had a hard time editing speech right then.
His level of observation was telling him he was fighting a loosing battle, and to a military man that was unacceptable. He needed to change his tactics.