The earliest pioneers of the video game medium did not give a shit about storytelling. Your character moved from point A to point B, occasionally murdering enemies for no reason -- there, that's your entire plot. But as the medium evolved, the developers began telling more and more complex stories, which posed a problem: How do you reconcile the mindless insanity of your franchise's early chapters with the sophisticated plots of today?
The answer is: not very well. Sometimes, the more they try to make sense of a video game's story, the more it becomes a convoluted mess only a complete maniac could understand. That's how we end up with continuities (if you can call them that) like ...
5Metroid -- Samus Has Killed The "Last" Metroid Like Three Times
The premise of Nintendo's Metroid is basically Ridley Scott's Alien as filtered by Japan: You're a kick-ass lady in robot armor trapped in a space labyrinth full of aliens, most of which look like sentient hors d'oeuvres. Couldn't be simpler, right? Unfortunately, the Metroid series' continuity is about as convoluted and hard to navigate as these games' maps.
All told, Nintendo has released nearly a dozen titles in the Metroid series, spanning 25 years.
Of course, that's in real-world time. In Metroid time, only about two weeks has apparently passed between all the games, because the protagonist, Samus, looks exactly the same age in all of them. This is in contrast to series like Half-Life (Eli and Kleiner noticeably age between HL1 and HL2) and Metal Gear (the craziest plot they could do next would be Solid Snake maintaining an erection). The seemingly short time span covered by the series is contradicted by the fact that "Samus kills the last Metroid" is an event that happens three separate times, in addition to murdering enemies like Ridley and Kraid several times each.
The anxiety of coming back to life so often makes poor Kraid overeat.
We might have a better idea of how much time passes if the series' canon wasn't a Gordian Knot of discontinuity. The original 1986 Metroid (and 2004's Metroid: Zero Mission, which is just a tarted-up version of that game) comes first in the chronology, but after that, it quickly devolves into chaos. The Metroid Prime trilogy (2002-2007) allegedly takes place between Metroid and Metroid 2 (1991) -- except that, no, that can't be right, because in Metroid Prime there are log entries that refer to the destruction of the planet Zebes, and that doesn't happen until Metroid 2's direct sequel, Super Metroid (1994). This same bit of information about Zebes is reiterated in the official Metroid Prime comic, where Samus is also surprised to find a live Metroid ... even though she doesn't kill all the Metroids for the first time until Super Metroid.
How can we enjoy Metroid Prime Pinball unless we know where it stands in the canon?!
It's a tangled mess, to say the least. One blogger painstakingly laid out the events of each game in chronological order, and the best thing he could say about it is that it's simpler than Zelda. Which brings us to ...
4Legend Of Zelda -- Nintendo Is Clearly Fucking With Us At This Point
While the Zelda series has always been second fiddle to Mario, Zelda makes up for it by having a continuity that was probably the topic of Stephen Hawking's doctoral thesis. The exact timeline of the Zelda games has been causing schoolyard arguments since the beginning, but there was a time when it was possible to make sense of it all without a PhD in nerdiness: You had The Legend Of Zelda (the original), The Adventure Of Link (the sequel), A Link To The Past (prequel, duh), and Link's Awakening (sequel to the prequel). See? Pretty straightforward.
It was only when Ocarina Of Time (prequel to the prequel) and Majora's Mask (sequel to the prequel to the prequel) arrived, with their fancy 3D graphics and enticing polygon boobs, that we started wondering how one person -- or elf or whatever the hell Link is supposed to be -- could fit all those adventures into one lifetime. Nintendo's answer is that he didn't; it was different guys with the same name and same predilection for Robin Hood fashion and night caps.
This is when the games abandoned any pretense of adhering to continuity in any recognizable manner (i.e., a series of events that progresses in a way that makes any goddamn sense). We got two games that happened at the same time and acted as prequels to the sequel to the original's prequel, followed by a further sequel/prequel that didn't seem to fit anywhere on the timeline. It wasn't until 2011, 25 years after the first Zelda game, that Nintendo even released that timeline, which finally helped clear everything up. Wait, no, it just confused the fuck out of everyone.
The "Adult Era" is a lot less exciting than it sounds.
It turns out that the events of Ocarina Of Time split the Zelda series into three timelines: The first assumes that Link got defeated in Ocarina, leading to the "Era Of Decline," meaning that if you got to the Water Temple and said, "Fuck it, I'd rather play Duke Nukem," the destruction of Hyrule is exclusively your fault. In the second timeline Link won at the end of Ocarina and got sent back to his childhood, explaining why, in some games, we meet a prepubescent Link with disturbingly well-developed combat skills. The third timeline has Link defeat Ganon but continue on as an adult, because there were still some adult-Link games that needed to be explained away, we guess. If you're still confused, then we completely forgive you, princess, because this shit makes no sense. Here, maybe this video will help:
It's convoluted to go alone! Take this.