The events of Peace Walker and the Clone War eventually lead to some of the most tragic events in Metal Gear, and the further disfigurement and moral decay of the hero.
At the end of Peace Walker, first he is betrayed by Paz, who he assumed was an innocent believer in peace. She takes control of Big Boss’s Metal Gear ZEKE in order to try to frame MSF by launching a nuclear device; the event makes Big Boss more on guard, and willing to morally compromise on some of the contracts his soldiers will take in order for his dream of “Outer Heaven” to survive.
Palpatine meanwhile begins to twist Anakin Skywalker into distrusting the Jedi, and play on his fears about his nightmarish vision of his wife, Padme dying during childbirth.
Shortly thereafter, a carefully organized trap changes the direction of things. Palpatine orders the Clone troopers to kill their Jedi superiors, whereas Cipher-drawing Big Boss away on a rescue mission during an important “inspection” of his HQ Mother Base-attacks and destroys mother Base, killing most of the soldiers and some of Snake’s Peace Walker allies, including Paz.
It should be noted that unlike Palpatine, Major Zero is not directly responsible for what happens; in fact one of his subordinates-a disfigured commander known only as “Skull Face”-is behind it. Zero eventually slips into a coma for the next twenty years, although his organization lives on, both as Skull Face’s force of XOF and the AI and gene manipulations of his subordinates Dr. Clark and Donald Anderson. Although there still will be some Palpatine comparisons before the saga ends.
He’s somewhat closer to Palpatine in his evil, and of course Palpatine himself eventually carries the scars, when the Jedi figure what he’s up to and Mace Windu directs the lightning back at Palpatine, warping his skin into the twisted face we remember from Return of the Jedi.
The trap-his “Order 66”-eliminates the Jedi, and also has Obi-Wan away from Anakin at a critical time, allowing Palpatine to finally twist Anakin into Darth Vader, who participates in the order, taking out the Jedi’s temple. Anakin’s final look however have to wait.
Eventually of course, Anakin’s former mentor and friend, Obi-Wan, catches up to Anakin and during the duel on Mustafar, badly maims him and Anakin is further burnt up by the volcanic lava. Although He’s still alive.
As the attack on Mother Base ends with it sinking into the sea, it’s revealed that Paz-rescued from the site where Snake infiltrated, is booby trapped, and as she explodes, the helicopter is destroyed, with Big Boss, a medic, Kaz and Chico caught in the explosion.
Both fiery fates will bring us to the next chapter.