Sorry if I'm late to the party on this but I didn't play MGS 5 Ground Zeroes Déjà Vu missions. In it, there's a task where you have to use a UV light to erase the logos of all Kojima-directed Metal Gear games, and only those. The rest of the MGS canon remains untouched.

As you wipe Kojima's existence from the game you get the following message:

There's also what appears to be a personal voice message from Hideo Kojima himself, saying "thank you for all your support" once you've completed the mission (and get told 'you must be a fan of Hideo Kojima games'). You can see a condensed run through of the mission here:

All this happened back in March 2014, long before any of the Konami/Kojima troubles surfaced. Since then Kojima's name has been removed from MGS games in general, including the actual box art for MGS 5 The Phantom Pain. Plus there's the cancelling of the Kojima/Del Torro Silent Hills which itself was prefaced by the disappearance of Kojima logos. It's heavily rumoured that Kojima is all but finished at Konami, seeing out the final production of MGS5 as a contractor. Whatever ultimately happens, it looks like he knew what was coming all along, effectively sneaking out a message in Ground Zeroes. It's certainly going to be interesting to see what pops up in MGS 5 The Phantom Pain arrives.

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