Monkey is a genetically engineered man, an enhanced clone created by Pyramid
He may be forged by many years of surviving alone, but Monkey's strenght, resilience and agility look more often than not superhuman. He may have been completely created in a laboratory, or be subject to genetic modifications when he was very little, and at least part of his memories be not real. Pyramid wanted to create sort of a Super-Soldier for his cause, so what better than a bigger and stronger version of himself? However, Pyramid ended up putting a small part of his conscience that considered his cause wrong into the clone, which escaped his control. The clone spent some time confused, his mind completely blank, surviving, until he became the Monkey we know. That would explain why Monkey, after fighting so fiercely until then, was falling prey to Pyramid's illusion quite easily near the end of the game, and why both characters are played by Andy Serkis. Pyramid is an Egomaniac and Started the Robot War that destroyed civilization
What do we know about Pyramid? We know he is behind the slavers who have been using the Mecha to abduct, enslave, and entrap people within hie Lotus-Eater Machine. From this we can extrapolate that Pyramid was somehow involved in the creation and control of the Mecha during the War, how else could he possibly have gained control of them. So this begs the question why? Well the simplest explanation is the most likely. Pyramid has a Savior Complex and created this apocalypse so he could "save" humanity. This mixed with I Can Rule Alone also explains why his robots are so murdery and why he whipes out Trip's village. If he can't rule over humanity no one will.