Hideo Kojima's Metal Gear Solid franchise is not only one of the longest-running video game series of all time, it is also one of the few that kept the same continuity through out. The likes of Super Mario and Final Fantasy are slightly older, but each of those games are standalone projects that don't really follow through on one story line. Given that the timeline runs through more than seven games, the plot does get a little complicated. To the studio's credit, most story lines and characters are resolved by the end of the massive saga.
With that being said, a select few characters left the franchise unexpectedly, giving fans no indication on where they went afterwards. The ten listed below did just this. It is a shame, too, since some of them were beloved, charismatic personalities who fans would have welcomed back with open arms.
Big Boss runs into Cecile in Costa Rica during Metal Gear Solid: Peace Walker. She isn't that important to the story after the initial encounter, but her conversations about French culture are thoroughly amusing. The character is actually based off a real-life woman with the same name, who was working with Konami before and during Peace Walker's development.
During Ground Zeroes, Miller mentions all civilian personal being evacuated from Mother Base because of the upcoming inspection, which would include Cecile. She is never mentioned afterwards but one can assume she spent the rest of her days in Paris. It would have been nice to see her come back, though.
9 Nastasha Romanenko
Nastasha Romanenko helps Solid Snake during the Shadow Moses Incident (Metal Gear Solid). The Ukrainian-born weapons analyst briefs the character on all of the weapons they acquire, and also discusses the dangers of nuclear weapons with them. She has such a strong disdain for nuclear weapons because she was born in Pripyat and directly suffered from the Chernobyl disaster, having lost both of her parents from the event.
After the events of that game, she goes on to write the in-universe novel In the Darkness of Shadow Moses, using the proceeds to help fund Snake's and Otacon's activities. However, she is never seen nor heard from again.
Amanda fights side by side with Big Boss in Peace Walker as she and her unit become an essential part of Mother Base. They came to Costa Rica after they were forced to leave their native Nicaragua. After Peace Walker she heads to Cuba, where she fortunately evades the tragic fate of Mother Base.
In the nine years between Ground Zeroes and Metal Gear Solid V: The Phantom Pain, she heads back to Nicaragua, never interacting with Big Boss or Miller again. One would think she'd have some part, especially after her brother's death, but The Phantom Pain swept a lot of characters from Peace Walker under the rug.
7 Beauty And The Beast Unit
This one resolves immediately if Snake chooses to fight them with lethal force. If he knocks them out instead, they simply doze off to sleep. Should the player do the latter, the bosses never return.
One would think the choice to kill them or knock them out would have some sort of effect on the game, but it doesn't.
Raiden got his own spin-off game in 2013. Metal Gear Rising: Revengance was a wild take on the series, but kept truer to the spirit of its source material than initial impressions led one to believe.
Unfortunately, it doesn't look like a sequel will happen any time soon, if ever, leaving Raiden's story woefully unfinished.
5 Ellen Madnar
Ellen Madnar (or "Elen" depending on which version you're playing) is Dr. Pettrovich Madnar's daughter. She was kidnapped and used as a bargaining chip to get the doctor to develop the Metal Gear during the debut title.
She was thankfully saved and promptly never heard from again. Her father briefly mentions her in the sequel, but it does little to wrap up her story.
4 Code Talker
Code Talker debuted in The Phantom Pain. He provides interesting commentary that dwells on the game's themes, like identity and importance of language in culture.
Unfortunately, he falls victim to the game's painfully unfinished state. If anybody wants to know how he is currently doing, all they have to do is boot up a finished save file of the game and say hi.
Sokolov appeared to have died in Metal Gear Solid 3: Snake Eater after Volgin beat him to a pulp off camera, but Portable Ops reveals that he survived the encounter. Throughout that portable entry he assists Snake from the shadows before revealing himself to the player.
He probably spent the rest of his days with his family in the United States. Given all that he has been through, the scientist deserved some rest.
2 Dr. Pettrovich Madnar
After the scientist betrays the player in Metal Gear 2, Snake incapacitates him. Fast forward to Metal Gear Solid 4: Guns of the Patriots, and Otacon nonchalantly mentions him when finding a doctor to help heal Raiden's injuries.
Snake doesn't even seem to raise an eyebrow at the name, though, making one wonder if it is even the same person or if they just happen to have the same name.
1 Holly White
Holly assisted Snake during the disturbance in Zanzibar. She was a CIA agent using the cover of a freelance journalist.
The two seemed to hit it off, but the relationship stopped abruptly after Snake went to Alaska. No-one really knows what happened to her afterwards, though it would be nice to imagine that she lived a peaceful life.