The main story for MGS4 was an absolute clusterfuck. Metal Gear has had confusing stories in the past (like MGS2, for example), but with enough looking into of the fine print, you can make some sense into it. No matter how hard I try, I still can't figure anything that goes on in the main story. I think what really makes everything come crashing down, any hope the story had of making sense, was with Big Boss's return in the epilogue. From a story standpoint, Big Boss was only there to clear up anything that didn't make sense in the story, but in the process, he only makes it MORE confusing than ever. First off, how does he come back? I understand his new body is made of parts from Liquid and Solidus, okay that's understandable. But how does he know pretty EVERYTHING that happened. He claims Naomi told him. When? She died back in Act 4, what did she have planned to be sent to you after the Patriots were destroyed. Plus, where was Big Boss? What super secret Patriots facility was he trapped in before they fell that he: Got new body parts for himself, found and kidnapped a now old Zero, find out Snake was at Arlington, and make it there to watch Snake attempt suicide. And we've only scratched the surface. Big Boss mentions that Ocelot's Liquid persona was nothing but a

to fool the Patriots. How does he know this? Keep in mind, Big Boss, Naomi, EVA, and Ocelot's goal was to end the Patriots' reign. In other words, their entire goal was to get their asses kicked by Snake. All the shit you saw them do for 5 Acts was all so they would lose and the heroes would destroy GW, and by extension, JD. Finally Snake's unstable version of FOXDIE. Naomi said that in half a year, Snake would essentially become a weapon of mass destruction, causing everyone around him to be killed by the virus. BUT NOW, Big Boss said that the new version of FOXDIE planted into Snake's body by Drebin destroyed the old version, meaning he's safe and doesn't need to commit suicide. That's a pretty big thing to leave out and not tell Snake, Naomi! It's not like Drebin did this late in the game, this was THE FIRST ACT. This pretty much implies that Naomi made Snake turn even more nihilist for a joke. Much like this game's story.
And you know what? I still love MGS4. The story was terrible, and yet I feel it had some of the best character interactions in the series yet. The sub-plots are what hold this game together. Snake being forced to come to terms with his accelerated aging is something that's so hard to watch, the scene where Naomi sees how decayed Snake's body has become was absolutely well done. Snake has practically shut out everyone important to him in his life, despite people like Otacon and Meryl still trying to stay close to him. The only thing Snake clings to are his cigarettes, despite the toll they take on his health. They actually successfully made tobacco, of all things, an important piece to what Snake has become. Despite how confusing the epilogue is, Big Boss and Snake reconciling I feel is one of the most emotional scenes in video game history. Just watching Big Boss disarm Snake, hug him, and say "Let it go, my son." was such a powerful scene. There's also Big Boss's death long after on the Boss's grave. Finally reconciled with his son, Big Boss's last words are, "This is good....isn't it?" Scenes like that are what keep MGS4 out of my shit list and why I still feel it's a game worth playing.