So at the end of the game, you get a tape explaining that you are not Big Boss, but an exact duplicate created by Zero to protect the real Big Boss from his own organization. This scene is really really good, and I love Kiefer's mocap work when Venom Snake smirks and looks at himself in the mirror with this look of power.
But the last few seconds of this scene are extremely important! When he flips the tape over, there's a time jump to 1995. How do I know this? Be perceptive; in the reflection of the mirror, there is a Diamond Dogs emblem on the bathroom door.
However, when Venom flips the tape over, that emblem becomes an Outer Heaven logo, and outside you can hear gunfire and chaos. What's the other side of that tape labeled?
Operation N313 aka the operation Solid Snake goes on in Metal Gear 1.
...
It can be safely assumed that whatever is on that N313 tape, Venom doesn't like it. He reads the info and immediately destroys a mirror in rage; that does not sound to me like the reaction of a happy man in a healthy partnership. Given the info we have, it can be reasonably assumed that Big Boss and Venom communicate through those cassette tapes; it can also be reasonably assumed that towards the end of Metal Gear 1, Venom Snake becomes aware of the fact that Solid Snake is coming to kill him and tries to sabotage that operation. During the game, your CO is Big Boss. He's basically the Campbell of Metal Gear 1; he gives you hints and suggestions on what to do. But suddenly, towards the end of the game, Big Boss contacts you on a new frequency and begins giving you bogus advice to try and sabotage your mission.
Real Big Boss's frequency: 120.85
Venom Snake's frequency: 120.13
This second Big Boss on the new frequency is Venom Snake trying to stall Solid Snake's mission. Now, what we see in MG1 is that the entire time, Big Boss is helpful in assisting Solid Snake in his mission to destroy Outer Heaven. We also know that Venom Snake contacts Solid and tries to stop the mission. If Big Boss didn't want Solid to kill Venom, he would have also worked to stop the mission, not assisted the whole time.
It isn't clear, and it will never be clear, what Big Boss's grand plan was for Operation Intrude N313.
As it stands in canon now, he expected Solid Snake to fail. Given the new information about Venom Snake, his motivations become even more nebulous. Killing Solid Snake is obviously in Big Boss's favor, but so would killing Venom Snake. Why? Venom Snake is one of the few individuals who knows of Big Boss's double and if he is capture alive would likely raise many uncomfortable questions for Big Boss in regards to his position within FOXHOUND.
The Outer Heaven uprising is intended to be a rebellion against the Patriots, but at some point it may have become obvious that it was going to fail. Venom Snake doesn't get the N313 tape until Snake has spent some time on his mission (you can hear him fighting outside the room Venom is in). At this point, it wouldn't be unreasonable for Big Boss to assume that the uprising was a failure, and that ultimately, the Patriots would destroy Outer Heaven. If Venom was captured, it is possible they could discover Big Boss's involvement in its founding.
So what about the damn MSX tape?
I think the tape contains Venom Snake's final mission: to die for the Big Boss legend. If Venom gives his life and takes responsibility for the uprising, Big Boss will be able to remain undercover and unharmed, ultimately allowing Venom to complete his mission as a lightning rod for Big Boss.
In the end, Venom gets the same mission that the US handed down to the Boss in MGS3: he is to die for his cause and will go down in history as a war criminal. No one will know who he was, no one will know what he sacrificed. His life, his face, his ideology, everything was to be taken by Big Boss and his legend. Big Boss does literally the same thing that the Philosophers/the US did to the Boss, the very thing he swore to stop so many years before.
Venom gets angry and rejects this mission; he punches the mirror and contacts Solid to try and stop the inevitable. In the end, Venom does what the Boss doesn't: he rejects his mission and implicates Big Boss in the whole thing. He tells Solid that he is Big Boss, causing Solid and everyone else to think that Big Boss had double crossed them and was simultaneously the leader of Outer Heaven and the CO of FOXHOUND, thus blowing Big Boss's cover. Solid kills Venom Snake, and Big Boss goes into hiding to build Zanzibar Land. And well, the rest is history.
