Sonic and Knuckles
In Sonic the Hedgehog 3, Knuckles (the red one, with the knuckles) thought Sonic was attempting to steal the Master Emerald, and that the mad scientist, Doctor Eggman (who is REALLY unfortunately named because c'mon, it's not like his parents knew he was going to be shaped like that), was trying to protect it.
Knuckles worked AGAINST Sonic and FOR Dr. Eggman throughout the game and was someone you had to fight before boss battles or as a boss battle himself.
However, Dr. Eggman had lied to Knuckles, and was planning to use the Emerald to repair his space station, the Death Egg (which is a little more unsettling than a Death Star purely because of how messy it would be if it exploded).
In Sonic & Knuckles, the next game, in the Hidden Palace Zone, Eggman's betrayal was revealed when he stole the Master Emerald with a modified Egg-O-Matic (just one of his many egotistically branded weapons/items) and attacked Knuckles.
Since then, Knuckles has repeatedly joined Sonic and Tails throughout their many adventures to help stop Dr. Eggman. No word on what Knuckles thinks of Tails, but he probably hates him just like the rest of us.
Master Chief and the Arbiter
Master Chief of the Halo Franchise, is a super soldier bent on saving the world from the invading "Covenant" who are looking to take over and destroy the world based on religious beliefs, unlike anybody we have ever heard of.
Here's the story:
So, the Supreme Commander of the Covenant fleet sent to destroy a human vessel fails in the first Halo game (if you beat it), as humans overtook the ring in a resistance and destroyed it to prevent the spread of the horrible, horrible "Flood".
As Halo 2 begins, this commander is branded a heretic and a traitor for failing his mission, because aliens are insanely brutal like that, but is spared just before his public execution and then became "The Arbiter", because that's what you become when you fail to destroy all sentient life.
During his first mission he is betrayed by a species on the same side (The Brutes, aptly named), but of lower "rank" in their caste. That's right, not only do these aliens speak English, but they have Caste systems... medieval social structure and f*turistic ships... no wonder they're pissed.
He is then saved, along with his nemesis Master Chief, by the very thing the humans were fighting, the Flood intelligence called "Gravemind".
After being rescued by Humans, The Arbiter joins their side against The Covenant, who has betrayed him, because hell hath no fury like an Elite (his race) scorned.
He and Master Chief fight side-by-side throughout the rest of Halo 3 and save the world together.In this video: the first episode of the classic Machinima series Arby 'N' The Chief, which puts The Arbiter and Master Chief together into an apartment as roommates, even though Master Chief (in this show) is a complete and utter douchebag, which makes this hilarious (at least to your average Halo fan )
Scorpion and Sub-Zero
In the first Mortal Kombat, Scorpion is a demon from the Nether Realm who throws spears and has a skull for a face, as well as excellent ninja skills.
Sub-Zero is basically Ice Man .
Sub-Zero (the blue one), the original, killed Scorpion and sent him to the Nether Realm (a kind of hell where, apparently, you can become a ridiculously awesome badass). No idea why anyone would be pissed to be sent there. Who wouldn't want a badass SKULL for a head (one that we could brandish without dying).
Mortal Kombat II:
Turns out, Sub-Zero (a title that is passed down, apparently) is now the little brother of the guy who originally killed Scorpion and sent him to this factory-O-awesome known as the Nether Realm.
Scorpion vowed vengeance on the person who sent him there, not knowing this Sub-Zero was the old one's little brother (as of Mortal Kombat II), but in Mortal Kombat II, Scorpion finds this out, felt really bad and decided to protect Sub-Zero instead, just to atone for slaying his kin in the other Mortal Kombat (since he found out that this Sub-Zero was actually a pretty stand up guy).
Since then, Scorpion jumped teams, stopped working for the evil Emperor Shao Kahn (KAAAAAAAAAAAAAAAAHN!) and decided to start working with the humans (or people from the Earth Realm) to kill this complete and total dick.Here's a clip of them from the best film ever made: Mortal Kombat (starring the guy from Beverly Hills Ninja), showing Sub Zero and Scorpion getting pretty cozy, teaming up on a young Bridgette Wilson.
Donkey Kong and Mario
These are two of the most on again off again enemies/friends (or frienemies) in video game history.
They start as bitter rivals for the affection of a woman when Donkey Kong kidnaps Mario's then girlfriend Pauline (who he later dumped to pursue royalty).
To get revenge Mario kidnaps Donkey Kong, whose plot is foiled by Donkey Kong's son, Donkey Kong Jr.
Apparently the ill will has been buried as Donkey Kong is regularly invited to Mario's Parties and sporting events. They even have a beer now and then .
But the rivalry sparks from time to time when Mario's old fling Pauline comes around, or whenever they happen to be in any kind of competition. But in any game where the Nintendo Universe comes together over something, they stand side-by-side.
Donkey Kong is Mario's friend in the same vein that The Hulk is anyone's friend. Sure, he saves people's lives, saves entire cities and goes through entire journeys in the name of good. But as soon as you piss him off, Donkey Kong (and The Hulk) will turn on anybody on a dime.
This video is a great example of this, as Donkey Kong is sitting at home all day, obviously unemployed, and falls in love with a toy of Mario. He tries to go to the store to buy his own, but they are all sold out. So, in classic Donkey Kong fashion, he goes to the Mario Toy Factory and steals all of the toys.
Mario's mission, then, is to get all his toys back. This is why they fight. Because of a lack of communication. Mario ends up giving Kong one of the toys and everyone is happy.These guys are the classic definition of "Frienemies".