This is just my attempt to clear up the plot confusion in MGS3 - specifically about why the Boss and Ocelot were trying to kill Snake (Big Boss) if they were ordered to aid him the whole time in retriving the legacy and allow him to kill the Boss herself. These are my theories:
1. Why was Ocelot trying to kill Snake? - Ocelot's grudge against Snake had gotten the better of him and he was disobeying his orders. This is why the Pain attacks Ocelot and his men during his duel with Snake at the canyon, and why the Boss later breaks his revolver.
2. Why were the Boss' Cobras trying to kill Snake? - This is less clear - my theory is that the Boss wanted them to test his strength - if he could defeat them then the Boss would know he would be an even match for her (if they had killed him then she likely would've had a backup plan, such as allowing Ocelot to kill her and take the legacy instead).
They may also have been attempting to buy time for the Boss so she could locate the legacy before Snake made it to Volgan's base.
3. Why does the Boss fight Snake at the finale? Why not just allow Snake to kill her - or just kill herself and let Snake take credit for it? - This is harder to explain; I'll assume that she just believed that as a soldier sucide was cowardice. And she knew Snake wouldn't voluntarily kill her unless she goaded him into it by fighting him to the death. If she had killed Snake, then again she probably would've had a backup plan in mind - such as having Eva or Ocelot kill her and take the legacy.
This is the best sense I can make of this anyway. Any thoughts here?