10 years later

Enigma was brought into the fold of the Vortigaunt Empire, thanks to the Church and the goodwill built up By Snake the whole process was smooth and quick. As for Earth, she too was brought into the fold. Though the inhabitants did put up a fight, America launched her whole nuclear arsenal at the fleet sent to oversee the process. The President and his cabinet cheered when the nukes hit the ships but immediately went pale when they saw that the ships were unharmed. Aside from that the Empire stabilised regions like China, South America, and surprisingly the Balkans. The Balkans did offer quite the challenge the Empire managed to end the conflict and instituted policies like rebuilding and repair, providing jobs, food, water, and high quality shelters. Effectively rebuilding the entire economy and ensuring peace in the region. Enigma and Earth became joint capitals of the galaxy with the empires and kingdoms of Enigma managing their part of the galaxy and Earths UN managing theirs. 

Brooks became an admiral of some renown when he joined the Vortiginian Navy and was given command of the fleet of ships tasked with patrolling and defending Earth. As for doctor Angela she became a famous plastic surgeon specialising in non-humans like elves or beastmen, it seems that she got some information on non-humans way before the rest of her field, perhaps as thanks from a certain mercenary. Since Enigma and Earth were brought into the fold of the Empire travel between the 2 worlds became as easy as taking public transport with stations set up on both sides to facilitate travel and to police any form of smuggling. Because of this when Fox decided to retire a few years after working with Snake she did some adventurer work in Enigma before becoming a teacher at the University in Sciencia specializing in monster hunting and combat training. Eventually she married Isaac, Snake attended the wedding and happily helped calmed the worried Isaac. Unfortunately for him Snake was smiling for a slightly different reason. When the married couple went to their home to enjoy their first night Snake slipped them a note left on the night stand laying out their family tree. You can imagine how they reacted. 

And what of Snake? Well after his duel with his master she brought him under her wing once again, now he works in the mercenary company formed by her who turned out to be the fifth Queen of the Vortigaunt Empire. Now Snake, Cherié and Fey roam the universe taking down wanted criminals, warlords, assassinating the leaders of other multi-galactic empires, and hunting the occasional monster. He also helps out Seraphim clones when they need a bit of fire support. 

Thus is the tale of the Merc in another world, now he roams the universe putting holes in evil people and occasionally rescuing good ones.