Spoil Without Context

[MassiveShock11]

The world where the story happened is actually a virtual world, and one of your friends is actually a computer program installed there.

 

[Lone_Garurumon]

It turns out that the villains are of the same species as one of your friends (previously thought to be the last of his kind) who got sucked into an alternate dimension by what is implied to be some kind of cosmic being after they nearly conquered the planet. So you and your friends go to this alternate dimension to reclaim the 7 Plot Coupons and the Master Plot Coupon, leaving the recurring villain (who has completely and utterly reformed by the way, oh yes, no plans to betray you here) behind in the ruins of his city. However, despite the 4000 years it's been since the villains were sucked into the alternate dimension, time flows much slower there, so once you've reclaimed the Plot Coupons and kicked the bad guy's ass, you return to see the recurring villain, who has rebuilt the city and now has an army, who then shoots down your spaceship in a cliffhanger that will never be resolved because Bioware has the rights to the original characters.
Your party then gives the end credits in a casual discussion for the lulz.

 

[Chidamari Sketch]

The true final boss briefly speculates that the first boss (who's also the first mini boss) might actually be the "God of the Everlasting World", which would mean that said first boss is a nemesis of the final boss

 

[Pyrax]

The protagonist has to seal themselves away with their younger brother to stop their reincarnated nephew. Meanwhile, another party member turns into a dragon.

 

[Lone_Garurumon]

The character that has been hyped up as the major villain and a huge threat is defeated in a boss battle identical to an earlier boss battle with a completely different character, and then just gets teleported away and doesn't come up for the rest of the story. Terrible waste really.

 

[TouyaShiro]

Your commander betrays you and then you kill some really angry bees in retaliation. Multiple times. May or may not come with insanely fast gabber. Yes, this is a recurring thing in the series which this comes from.

 

[Wispy Willow]

It turns out that the location that the entirity of the story revolves around was created by an alien to seal an ancient evil while said alien could guide humanity along the path to (eventually) besting said ancient evil.

Spoiler: Also...

 

[Lone_Garurumon]

It turns out that the recurring villain you thought was the bad guy all along was actually thrown in a cell by a creation of his who's shown up in several previous games, and has usurped his armada to gain power for itself. It wasn't out of nowhere though, there were hints, including a giant statue of the creation in a certain level that you're forced to look directly towards... Yeah, more people really should've guessed it than actually did.

 

[TouyaShiro]

The commander of the previous (canon) game is revealed to be behind this dastardly boss gauntlet. Then he sends you off to do it again, but MUCH harder this time. Even if you do reach the end... it's a thankless job.

I admit, I wish this expanded beyond just game endings, lol.

 

[Wispy Willow]

It turns out that the recurring villain you thought was the bad guy all along was actually thrown in a cell by a creation of his who's shown up in several previous games, and has usurped his armada to gain power for itself. It wasn't out of nowhere though, there were hints, including a giant statue of the creation in a certain level that you're forced to look directly towards... Yeah, more people really should've guessed it than actually did.

Spoiler

this song is the best kind of cheese and im ok with that

Anyway... It turns out that, while the main villian does manage to take over the world, that doesn't mean they know what they're going to do with said world.

 

[Chidamari Sketch]

The initial bad guy is a crazy-as-fuck priest who goes into a unreadably fast rant that ends up dumping one hell of a bombshell of lore before fighting you. After getting defeated, his ugly face is shown, which drives him in a violent fit of insanity, to the point where he summons his three generals just to drain their health to restore his own and hypnotize them into mindless rag dolls for him to use as weapons and meat shields. And after that madness ends, he forces his mind controlled allies into sacrificing themselves into an incomplete macguffin alongside himself in order to summon an apocalyptic god.

Said demonic god is heavily implied to be not only related to an infamous group of Eldritch Abominations, but is also heavily implied to be the creator of another macguffin from the Wii game that corrupted a character who betrayed you. Oh, and in the last phases, it occasionally dons the main character's face, as well as the aforementioned eldritch abominations' forms as well.

 

[Pyrax]

The giant tree worshiped by one of the main characters turns out to be evil, so they decide to beat it up. Dinosaurs and a possible alien are involved.

 

[Harryghost]

The two part ways in the end.

 

[Chidamari Sketch]

Your best friend literally committed suicide at the tutorial, and is now corrupted into a malevolent spirit by a demonic arachnid entity; the true identity of the tutorial voice. The only way for your friend to rest in peace in the afterlife is to let go of your bond with her and move on. Oh, and one of your arms gets severed cleanly off in the process.

 

[Harryghost]

In the end, she absorbs the mysterious woman's powers.

 

[Revenge of the Boyega]

They hold hands but it doesn't end well.

Mysterious, isn't it.

 

[AnimeboyIanpower]

The Embodiment of Humanity's Evils awakens on a boat made by people from the Moon, takes away the powers of the main heroine, who turns out to be a wolf, and is about to finish her off when suddenly everyone's prayers reach her and she defeats The Embodiment of Humanity's Evils as the sun rises...

 

[Revenge of the Boyega]

A slug-like entity is coughed up into the basin. It escapes into the drains and comes back later... with menaces.

 

[AnimeboyIanpower]

The initial bad guy is a crazy-as-fuck priest who goes into a unreadably fast rant that ends up dumping one hell of a bombshell of lore before fighting you. After getting defeated, his ugly face is shown, which drives him in a violent fit of insanity, to the point where he summons his three generals just to drain their health to restore his own and hypnotize them into mindless rag dolls for him to use as weapons and meat shields. And after that madness ends, he forces his mind controlled allies into sacrificing themselves into an incomplete macguffin alongside himself in order to summon an apocalyptic god.

Said demonic god is heavily implied to be not only related to an infamous group of Eldritch Abominations, but is also heavily implied to be the creator of another macguffin from the Wii game that corrupted a character who betrayed you. Oh, and in the last phases, it occasionally dons the main character's face, as well as the aforementioned eldritch abominations' forms as well.

Spoiler: "I know that one!"

It's Kirby Star Allies!!

A slug-like entity is coughed up into the basin. It escapes into the drains and comes back later... with menaces.

Spoiler: "I also know this one..."

It's Five Nights at Freddy's: Sister Location, isn't it?

You were made by the villain to serve as a replacement should he die.

Spoiler: "Lemme guess..."

Is it MegaMan Zero 3?

Gods, I love that final boss fight!!!

After having almost been killed by the former leader of the resistance he quit to save a girl from an evil company, a lightning-wielding psychic kid merges with a girl with butterfly wings, kills his former boss, and walks off into an uncertain sunrise...

 

[Lone_Garurumon]

Spoiler: "Lemme guess..."

Is it MegaMan Zero 3?

Gods, I love that final boss fight!!!

Spoiler

Close, it's Megaman ZX Advent.

The guy who was supposed to fix your friend has turned evil from exposure to the evil substance, and you wind up killing him... Probably... Leaving no-one who knows how to fix your friend.