At 10am (in Japan) Kojima’s count down website went down for a few minutes before being replaced by… another count down. The timer started at 120hours, and is set against the exact same background with a ‘5’ or ‘S’ still being occasionally silhouetted by lightening.

Unimpressed I was about to close the window when another lightening blot hit the scene illuminating a new symbol. This time what could be a ‘3’ materialised. Two more subsequent symbols joined the original 5/S and 3, one similar to a capital ‘E” and the final one a backwards ‘9’ or lowercase ‘g’ (see image below).

I am still unsure of the meaning; while the 5 still supports anther MGS game these new symbols do nothing to overtly support that. Indeed the font used is more in keeping with the ‘Zone of Enders’ typeface then MGS’s.

This new count down is ticking down to the same time on May 27th so again I will be logging in again soon after. Unfortunately speculation on line suggests that the final reveal for this project will be on June 1st at the start of E3, so maybe I will just be greeted by another 120 hour counter.

UPDATE - Leaks from 7-11 here in Japan about an upcoming PS3 magazine suggest a new MGS game for the system on the May 30th cover, which could be linked. Also some are speculating that the backwards 'g' is an '@' mark in this type face, making this read a message '5@E3'. (Source)

Source
Speculate about this on the forums