User blog comment:Weedle McHairybug/So, why did Big Boss react with confusion in regards to Cipher? (Spoilers)/@comment-70.126.138.92-20100825204126/@comment-67.247.235.100-20130422141757

Chiper is just a code name for "Zero" who was one of the founders of the Patriots as you are well aware. It's just another name for the Patriots just like La-Li-Lu-La-Lo.