And he gave it to Zero, so it's gone.
Eh there's conflicting lore on it.
During
Operation Snake Eater, EVA was supposedly successful in recovering the Legacy, but, unbeknownst to her, the film she obtained was actually a fake. This failure in her mission caused EVA to lose her reputation and credibility. The real microfilm eventually made its way into America's hands, thanks to the actions of Snake, The Boss, and the Philosophers' triple spy
Ocelot. However, the CIA were only able to recover half of the Legacy using the film, and it was assumed that the
KGB possessed the other half. Some time later, Ocelot eventually located the remainder of the Legacy, though he kept it for himself.
Warning: The following information is from outside
Hideo Kojima's core "Metal Gear Saga." It has some level of canonicity within the continuity, but reader discretion is advised.
[?]
In 1970, Ocelot and
Zero set up
Gene's
San Hieronymo Incident as a ploy to obtain the remainder of the Legacy. When Ocelot confronted the
CIA Director, the latter told him about documents which revealed where portions of the Legacy were located.
[6] Afterwards, Ocelot assassinated the CIA Director and obtained the other half of the Legacy, which was then used to fund the creation of
the Patriots.
Non-"Metal Gear Saga" information ends here.
During the
Peace Walker Incident in 1974, the Patriots told EVA that the Legacy had been put to "good use."
[7]
So, Ocelot handed over the first half of The Legacy that Big Boss was originally sent to recover, but kept the second half he found. But then it splits. One side says that both parts of the legacy were given to America/used to fund The Patriots and the other side says he kept it for himself.