If you're not averse to reading ten pages of spoiler tags I could tell you
.
But if you want the basic version...
The plant you play the game through on was really the new metal gear, at the end when you fight the smaller version of Metal Gear Ray the big version goes a little mad as Ocelot (who is actually Liquid Snake because he 'Lives on through this arm') attempts to pilot it and do nefarious deeds with it. So you get thrown off and somehow because of Solidus's intervention land on City Hall.
Plot holes ftw.