It's known that there is an entire third chapter that was cut from the game.
You can view what remains of it - it's estimated that only about 30-40% was completed befofe Konami pushed for a release - on YouTube if you search for "Episode 51".Snake goes deep into Africa - an entirely new location - to track down Eli, the Third Child and Sahelanthropus. He finds that Eli has released the vocal chord parasites onto the population and has created a Lord of the Flies-style society with the child soldiers. Snake finds that Eli has since hit puberty, making him vulnerable to the patasites. He offers Eli one last chance to rejoin society, but abandons him when Eli rejects him, thus explaining Eli's hatred of Big Boss. The final scenes show the Third Child removing the parasites from Eli.
It's also believed that Kojima had fifty unique missions in mind, each with four variations: normal, extreme, total stealth and subsistence.
Yeah I watched all of that on YouTube, the cut scenes give a pretty good idea how that would have gone down. I don't really feel we're missing too much on that specific part of the mission, it would have just been a sneak through and then take down type job I'd imagine but perhaps Kojima had more planned, sub-missions before the parts depicted in the cutscene.
Also in that 'Coming in Chapter 2' video at the end of chapter 1 I'm sure it previewed things that never happened in those last missions but maybe I'm wrong, I've not watched it again to check.
It did seem like a few random subsistence/extreme missions were left in just to round it to 50, pretty clear they planned to do more than that.