Did You Know Gaming? Forums

Metal Gear Solid 4's ending was a lot different to how it is now, In 2008, the video game Metal Gear Solid 4: Guns of the Patriots contained in its end credits the song Here's To You released in 1971 as part of the soundtrack of the film Sacco e Vanzetti. In the game's original ending, the two main characters, Solid Snake and Otacon, were supposed to be executed for war crimes that they did not commit. Despite the change in its ending, the song remained. The song may also be relevant due to the situation surrounding The Boss, and to a lesser extent Big Boss.

So the ending is supposed to be Solid Snake and Otacon, being executed for war crimes that they did not commit.

Source can be found via google.