the guy hired by the Camerlengo to pretend to be the leader of the reborn Illuminati looked a lot like Otacon, and from there, I realized that the movie shared a lot of parallels with Metal Gear Solid.

Robert Langdon = Solid Snake
Victoria Whateverthefuckhernameis = Meryl Silverburgh
The Camerlengo = Liquid Snake
The Illuminati = The Patriots
The Catholic Church = The Philosophers?
The Fake Illuminati Leader = Otacon
The Antimatter Bomb = A new Metal Gear

So therefore, if we do the appropriate character replacements, the new story becomes:

Snake is relaxing at home in the U.S. when he suddenly gets summoned to The Vatican in order to help the Philosophers defeat the Patriots, who have been threatening them. This time, the Patriots have stolen the prototype of a new Metal Gear and are threatening to use it to destroy the Philosophers. When he arrives in Rome, Snake meets up with Meryl, who had been watching over the creation of the prototype Metal Gear, and together, they try and stop the Patriots' evil plans. As they try to find the Metal Gear prototype, they realize that Otacon has gone rogue and appears to be behind the entire plot. After Otacon dies in a car bomb, they find out that the man who has been helping them the entire time is none other than Liquid Snake, who actually orchestrated the entire thing.