The whole plot with Zero/Cipher becomes infinitely more interesting if you know what happens in future games.

MEGA SPOILERS if you haven't played the other MGS games:

Note: I have not completed MGSV so I don't know what is actually going to happen, but here's what I know from having beaten the other major games in the series.

• Major Zero is the mastermind behind a group called The Patriots (aka Cipher). He created this group alongside Big Boss, Ocelot, EVA, Para Medic, Sigint, and several other prominent characters. Big Boss left the group after they stole his DNA and created three clones (The Three Snakes: Solid, Liquid, and Solidus). Since then, Zero has basically been trying to get Big Boss back on his side, or at least use his skills from behind the scenes for his own purposes.
• Some time after that event, Zero went inactive. He is currently (during the events of MGSV) on life support and is very likely NOT giving any orders that have to do with hunting down Big Boss. Due to his failing health, Zero created a series of AI's to run Cipher/The Patriots without his input. He programmed these AI's to shape the world in the Boss' vision (Big Boss's mentor). These AI's basically go rogue in Zero's absence and start doing whatever they want, including using Big Boss as a pawn in their plot for world domination.
• I believe that the Patriots AIs are the ones actually in control behind the scenes of this game. They're the ones supplying weapons and ordering the creation of new Metal Gears. I really wonder if/how Big Boss ever finds out about this, since we know he figures it out by the end of MGS4.