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Since the San Hieronymo Peninsula is mentioned in Peace Walker and its otherwise never explained where Big Boss got his start up funds and first recruits (besides Kaz), Id say the game is semi-canon.
I propose the canon elements are:
1. FOX did rebel at the San Hieronymo Peninsula.
2. Big Boss was brought from retirement to put it down.
3. He did meet up with Campbell.
4. He did recruit former members of FOX and Russian Special Forces stationed there.
5. He successfully stopped the rebellion and officially dismantled FOX.
6. He acquired the resources to start the MSF (while PO explains it as Gene giving him the resources, Id figure from the poor state the MSF starts in that the MSF just looted vehicles, weapons, and equipment from the base). This included that sneaking suit, since the MSF version looks so similar.
7. He helped Campbell found FOXHOUND, before departing again to link up with the MSF.
The rest I wouldn't consider fully canon. Gene and the Successor Project, Elisa/Ursula, etc. But most especially Metal Gear RAXA, as its not a Metal Gear as described and designed by Granin.
Metal Gear = bipedal, nuclear armed tank, small enough to launch a nuke without being detected, able to defend itself from infantry and other smaller forces, most commonly with its nuclear cannon mounted on a single side.
RAXA = a short range VTOL with multiple missile pods in the wings, made to be launched into enemy territory via an ICBM, fly itself into an optimal position, and deliver its nuclear payload in a suicide attack. Besides its 4 landing stands, its not even a walker. Thus doesn't even classify as a Metal Gear.
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