Get ready for a long one.
Set after Rising. It starts with a prologue mimicking the MGS2 tanker chapter. You play as Raiden going on a covert sneaking mission. What it is dosn't matter but it leads to him putting down his sword in favor of training new recruits for the reforming US Military.
We fade to 20 years later. A young 30 year old agent going by the codename of Snake is being sent to infiltrate a large military base in Russia (not like MGS3, the cold part of Russia) that has bean taken over by a military group known as The Seven Snakes. Seven clones of Solid Snake that are each engineered to embody one of Solid Snake's traits. Solid Cobra, the master tactician and leader. Solid Python, the best at sneaking and being unseen. Solid Anaconda, the one with the most physical strength. Solid Viper, the deadliest and most sadistic. Solid Mamba, the most intelligent. Solid Rattler, a master negotiator with a silver tongue. And Solid Boa, a master of torture and interrogation. The pressure of living up to Solid Snake's name and the constant use in combat from a young age has left each Snake mentally scarred in a unique way. The new Snake lands and after establishing a base in the... base, she is revealed to be a woman and her code name is fully revealed as Silent Snake. Raiden and 4 other characters I've yet to create are on codec. After venturing further into the base Silent Snake finds what appears to be young Solid Snake. He's disoriented and attacks Silent. After being tranqued your science codec member is able to deduce he is a clone of the original Snake with his implanted memories. Solid Snake travels through the base with you God of War and Last of Us style, sharing wisdom and helping you defeat the Seven Snakes. Along the way, mimicking Gray Fox and Mr. X, a mysterious female solider named Dark Raven appears to assist you many times. She uses Raging Raven's jet pack and Vulcan Raven's Gatling Gun. After several encounters she is unmasked and revealed to actually be Solid Python, revealing that she's a transgender woman who has been using a refined version of the parasite cure from MGSV to temporarily change sex and assist the heroic Snakes. She is forced to "Overdose" by Boa after this revelation, making the change permanent. She is airlifted out of the base and sent back to Silent Snake's chopper for medical assistance. The final story beat comes during the battle with Solid Cobra. During a famous Metal Gear plot dump, it's revealed that Silent was supposed to be the eighth Son of Snake. But when the randomized DNA turned her female, she was deemed defective and was going to be euthanized. Thankfully Raiden offered to adopt and train her. This personal relationship turned her into the most well rounded and stable Snake. Solid Cobra also reveals that this base has been experimenting with biological enhancement drugs modeled after the Metal Gear and Cyborg Ninja programs, as well as his severe daddy issue complex seeing Solid Snake as an absent father figure. He says that he is going to surpass and destroy Solid Snake and takes the Super Soldier formula labeled "Bio Gear" and assumes the form of King Cobra. After the final boss fight, the base is in flames and is going to explode. Raiden steps in at the last moment and rescues Silent, but Solid Snake stays behind. Declaring himself a remnant of the past that dosn't belong in this world. As the base explodes, the fallen Cobra is having a mental flashback to his childhood. He's crying out for daddy. Snake kneels down and comforts him. His last words being "It's okay. Daddy's Here". The final scene is Silent Snake and Dark Raven giving their mission report to the Army Cheif of Staff and deciding to form their own FoxHound.