I haven't played through each possible combination of choices but I have tested multiple of them and concluded that there are two mission branches that intermingle together.

Originally, I had a localised version of the game so I'll try my best to translate mission titles faithfully.


Table legend:

• If a mission is not filled in branch #2, it is identical to the mission in branch #1.
  
• Choices are highlighted and signified by the '+' sign. If you choose the first mission, you'll continue branch #1 and if you choose the second mission, you'll continue branch #2.

Note that beside the missions apparently common to both branches, missions #11 to #15 in branch #1 are equivalent to missions #12 to #16 in branch #2.

The total number of missions is 45 so I can somewhat confirm mr. Shawn Sanders's words in his review[www.gamerevolution.com]:

Originally posted by Shawn_Sanders:

With 52 missions in all, there's some nice variety here. But due to the branching you only wind up playing about 40 of those.