It’ll be until after Metal Gear Solid 4 and Metal Gear Online both have had their time in the spotlight before Kojima’s intentions are revealed. It’s hard to really take a guess at what sort of game Kojima might be doing, because between Metal Gear, Zone of the Enders and Boktai/Lunar Knights, he has quite a varied resume.
Initially, Hideo Kojima announced that he would be retiring as director of the Metal Gear series after Metal Gear Solid 3: Snake Eater, and would leave his position open to another person for Metal Gear Solid 4, as he had announced he would after Metal Gear Solid and Metal Gear Solid 2: Sons of Liberty. As a joke, the new director was announced as "Alan Smithee", but in R, a 400-page book bundled with Metal Gear Solid 3's Japanese "Premium Package", the director was revealed to be Shuyo Murata, co-writer of MGS3 and director of Zone of the Enders: The 2nd Runner. He has also contributed humorous easter eggs to Metal Gear Solid 2: Sons of Liberty and Metal Gear: Ghost Babel. However, it was announced that Kojima will be co-directing the game with Murata after substantial negative fan reaction, including death threats.