The entire epilogue. Everything is as wrapped up as can be, Tokugawa is paying dearly for his crimes while working alongside Becker, Becker himself is dead, as is Redwood, Karen is alive and well thanks to Jonathan providing the necessary bone marrow transplant for her, Dave and Kenzo have been avenged and the organ trafficking ring has been hit hard if not outright shut down. Jonathan prepares to leave Beyond Coast for Home and says his goodbyes to Ed Brown, but not before giving him a present: a picture of Ed drawn by his estranged adopted son Marc, who's come to love him as a father. This is enough to move Ed to tears of elation (and the player as well.) As Jonathan leaves, Meryl tosses him his cigarettes, with Ed reminding him to lay off them (Jonathan lights one up anyway while saying "We'll see.") Hell, Jonathan and Ed's final dialogue together caps off that scene magnificently:
Ed: Hey, Jonathan! We made a helluva team, huh?
Jonathan: You're a helluva friend, too.
The scene with Jonathan heading Home caps it all off with him watching one last BBC news broadcast from Karen, who's returned to her job after having been temporarily replaced with a hologram due to her illness.
Karen: Finally, I would just like to say how great it feels to be back following my leave of absence. Hopefully, that's the last we'll be seeing of my "evil twin." Thank you for all your support.
The last scene before the credits has Jonathan reading a heartfelt thank-you letter from Karen as well. There's even a Stinger right after the credits in true Kojima fashion, with Jonathan remarking that no matter how far they travel into space, humanity can never truly forget Earth, their birthplace, and will always watch over her.