- The End's last words and death.
- The ending of of the whole game and the death of The Boss was a very intentional example designed to show Naked Snake, aka Big Boss' Start of Darkness. When she is defeated and asks Snake to kill her, he aims a gun at her heart and the game waits for you to press the fire button. After spending the entire game hearing about and seeing traces of the intense bond that Snake shares with her, it is quite possibly the biggest Player Punch in the entire series.
EVA: Snake... the world will never know what she did. She was a real hero... She was a true patriot.
- And the later revelation that The Boss was a Fake Defector committing what she knew to be a Suicide Mission at the sacrifice of her honor for all time. One of the greatest heroes in American history will forever be regarded as one of the worst traitors. The last scene of the game is punctuated by the now-iconic image of Naked Snake's salute◊. There's a reason the image is the one highlighting the Tear Jerker page for the series as a whole.
- You don't see EVA's face for any of the last portion of the ending scene, but you hear her start to break down and sob. Listening to her voice cracking on the last part of her voiceover, coupled with the visual on-screen at that moment, makes it very hard to not get choked up along with her. The line where she chokes up doesn't help:
- The loud neigh the Boss' horse lets out upon finding her dead. Mourning its master.
- The flower petals in The Boss' death scene were extremely poignant, especially considering the different cultural connotations of the color white. In Western culture, white symbolizes purity and innocence, and is worn by the bride at weddings. In Eastern culture, it symbolizes death, and is worn at funerals. Red is also subject to such duality. Western culture views red as bloody and impure, while Eastern culture views it as a color of celebration. So the petals turning from white to red actually has two meanings: the first is that it symbolizes Naked Snake's loss of innocence as he inherits the title of "Boss" and becomes Big Boss; the second being that while The Boss' death is sad, she's moved on to a better place and is reunited with The Sorrow.
- The Boss' headstone has to leave her name out, with only "IN MEMORY OF A PATRIOT WHO SAVED THE WORLD 192X-1964" written on it.
- Another thing related to the flower petal turning white from red. Before the fight with her, the Boss said something along the lines of how her blood turned as white as snow while she was in Nevada. Red to white. Make what you will of it.
- The song "Way to Fall," which plays during the credits, is a very sad song, especially because the lyrics go so well with The Boss' death and how Big Boss feels.Son, you've got a way to fall,
They'll tell you where to go,
But they won't know...
Son, you'd better take it all,
They'll tell you what they know,
But they won't show...
I've got something in my throat...
I need to be alone...
While I suffer...
- The "Snake Eater" song too. Despite being surprisingly fun and upbeat, the song also foreshadows many events in the game including the demise of The Boss.
- There's something about The Fury's last words, especially the melancholic delivery, that are incredibly touching:The Fury: Mission Control, do you read me? I'm coming home!
- What makes it more poignant is The Fury in his final moments is remembering the day of his botched mission in space, where he burned alive upon re-entry. For one brief moment he saw the beauty of the Earth from space, before that vision was replaced by the world engulfed in flames. His sad intone of "I see the Earth" is him reliving the trauma.
- At the beginning of the game when Snake and the Boss have their Codec conversation. When you know all of what is about to happen, there is something heartbreaking about hearing Snake say, "it's good to hear your voice again."
- The Boss' speech before the fight against her, where she gives her backstory and a deeper understanding of her motivations. Even before finding out she's a Fake Defector, all of your thoughts that she's anything but a good woman should disappear at that point. Only making the fight against her and its aftermath more gutwrenching.
- Snake not uttering a word during his debriefing at the end, being too heartbroken over the information EVA revealed in her tape to even speak. As he leaves without saying anything, Para-Medic is visibly concerned.
- A tearjerker in hindsight, considering the quirky Mission Control characters all become Fallen Heroes in some way or another.
- Snake ultimately adopts the title of Big Boss, and attempts to carry out his interpretation of The Boss' will: A world where soldiers always have a place. In his quest, he alienates much of his old support team, plays along with the Body Double Zero gives him, and ultimately dies at his mentor's grave, alone with his sole surviving genetic son who stopped him twice decades before.
- Sigint, aka Donald Anderson helps develop Metal Gear REX, a concept eerily similar to a nightmare he had, and that he had wished would never come true, alongside the AIs that would eventually become the Patriots, taking on bribes from arms manufacturers to fund their development.
- Para-Medic, despite her objections towards human cloning during Operation Snake Eater, helps kickstart the Les Enfants Terribles project, under her real name, Dr. Clark. She ultimately dies at the hands of Gray Fox, who became the Shadow Moses Incident's Cyborg Ninja due to her experiments.
- Most tragic of all, however, is Major Zero. He forms Cipher mainly to carry out his own vision of The Boss' dying wish: where information was tightly controlled, ensuring the status quo. He alienates Snake when he initiates the LET project without his permission, and commissions the Patriot AIs, only to realize they were a complete mistake. In the process of trying to repair his relationship with Snake and salvage what he could before Cipher grew too big to stop, he ends up infected with parasites by Skull Face. He spends the last decades of his life in a coma, unaware of what became of his efforts, and Big Boss dies not knowing his old superior had tried to save him.
Tear Jerker / Metal Gear Solid 3: Snake Eater