You play as Liquid (Teenager, a few years after TPP (still has the same jacket, tho it barely fits)) After stumbling through the jungle surviving as a tiny African warlord for a few years you go off and find a facility that looks a lot like Outer Heaven from MG1. You the player realize that the plot around infiltrating it is BASICALLY the same as MG1 as well, tho modified to suit Liquid's motivations. The final reveal is not that Big Boss is the leader, but Quiet. Quiet has the Fear's body and is trying to use it to construct a new super solider to replace BB entirely out of Bees and Parasites. This soldier is known as Bee Bee. Liquid jumps in a nearby Metal Gear prototype and fights Bee Bee and looses, no explanation is given for why a pilot-able Metal Gear is at the base. Liquid is saved at the last second by Ocelot + Mantis, who Fulton him off. Ocelot reveals that the children you saved during the mission all have powers, and now your in charge of FoxCat, a group of teenage super soldiers with attitude who need to take on enemies no one else can fight. Liquid refuses, goes off to sulk about things and be a punk alone, when suddenly he is ambushed by Bee Bee, Quiet, and a Metal Gear Ray. The game starts glitching. Liquid wins using only the cool robot powers (like raiden's) he suddenly has, working with the other members of FoxCat, and following every word Ocelot says to the letter. The game seems to end in a crash before rebooting to show you getting an award from the POTUS for stopping the gravest of threats, and appointing FoxCat as an official US special forces group under Occelot. If you 100% the game theres a secret conversation where Occelot reveals he's made some modifications to the training program, and the new "S4" system will give the Patriots total control over the worlds PMF's, should they need it.

TBH I ran out of steam after Bee Bee, but I think that part is brilliant enough.