There have been several people who have dug up files from the pc version showing that there was a chapter 3 entitled "Peace" missing from the game, people also seem to have found that the rehashed chapter 1 missions as a part of chapter 2 were also added late into the game. This really shouldn't come off as a surprise, why in the hell would chapter 2 have more chapter 1 rehashed challenge missions than their own stand alone missions, why do we have to sit through random chapter 1 story content while playing new story content in chapter 2. I know its possible to avoid doing those missions and do side ops instead but it is still unarguably terrible game design, the rehashed challenge missions are classed as main story missions in the same list and anyone would think that these are required to progress the game. The game just looks and feels massively unfinished and rushed once you get through chapter 2, not that the game visually seems unfinished or anything, whats there is beautifully polished, but what isn't there is about half of the game.
Although I must admit it did take a bit of time for me to realize just how bad the problem seemed to be. I think the mindfuck of the ending initially made people unaware of how out of place that whole mission even is in the context of Chapter 2. The last two story missions of the game are "Shining lights, even in death" and "The Man who Sold the World." How the fuck do we go from Snake telling Kaz that they are wearing their comrades into battle to the revelation in the hospital. That's literally what happens and it is so atrociously jarring and paced. What we have here is the final mission of the game most likely, appearing about 25 missions before it should have. It's absolutely infuriating..... To go from the ashes scene to BAM!!! Waking up in the hospital again, time for the big twist. Absolutely terrible and inexcusable.
The Shining lights mission was likely the turning point that led into the third and final chapter which really showcased Venom Snakes descent. The eli mission perhaps being the end of chapter 2 or the beginning of chapter 3, apparently that mission was also to take place on a new map.
https://www.youtube.com/watch?v=-B4JIHh5Jqk Here is an unfinished version summary video that was included to show fans what should have happened, it was included in the collectors edition. Eli hijacking Metal Gear was obviously the most blatant plot thread left open so I guess they wanted to show the fans what they were unable to complete.