Plot-Mandated Friendship Failure

Robin: I'm going solo!! (storms off)
Commission Gordon: What the hell happened?

—Jim Gordon echoing the thoughts of the audience, Batman and Robin

This is when, just before the third act and when things are at their worst, the protagonist is abandoned by their best friend. Here's how it normally plays out:

It's been a long, hard road for the protagonist. They've fought their way through rising complications, twists and turns, and unexpected outcomes, yet are the furthest from achieving their goal since the story began.

Good thing they have their best buddy to help them when all other lights have failed.

Or not. Apparently the stresses involved with The Quest have taken their toll on the relationship, stretching it to the point of breaking. And then one last thing, one straw to break the camel's back, perturbs the protagonist, and in a moment of rashness, he lets loose a barrage of atomic Jerkassness on his best buddy.

Unfortunately the best buddy, the calm head and stalwart that promised to stick by the hero through thick and thin, he's got his breaking point, too, and the protagonist's last action just crossed the line. The best buddy abandons the protagonist, leaving them with nothing by way of support—and just at the worst possible time to boot. That is because the Plot-Mandated Friendship Failure is always set to go off right before the protagonist has to face his biggest challenge in The Climax.

Expect a change of heart and a last minute save by the best buddy in the climax, thus reinforcing The Power of Friendship.

A staple of buddy pictures, where the friendship drives the plot.

Compare Second Act Breakup, in which the relationship in question is a romantic one.

Examples of this trope are found in the following works:

Film

The Movie of Get Smart features this split between Agents 86 and 99.
The Green Hornet has a falling out between Britt and Kato over who gets the girl and who the real hero is. It culminates with an argument over whether they're a boss and employee, or friends. They make up in time to face off with the Big Bad.
In Shrek the Third, when Shrek and Artie are captured by Prince Charming, Shrek says how little Artie means to him. Artie seems very upset until, after Charming releases Artie, Donkey tells him Shrek did that to save his life.
The Lord Of The Rings: The Return of the King: Inverted. Just when he needs him most, Frodo sends Sam away due to Gollum's ploy. Moments later he's paralyzed by Shelob. Luckily, The Power of Friendship prevails. (In the book, they're just separated in the maze of caves.)
Monsters, Inc.: When Sully and Mike are banished to the Himalayas, and Sully's first concern is Boo, Mike tells him "you're on your own."
The Rush Hour movies feature this betwen Jackie Chan and Chris Tucker.
Shanghai Noon features such a split between Jackie Chan and Owen Wilson.
Wayne's World: After Wayne erupts into a total Jerkass and ditches him during a live taping of the titular show, Garth dumps him. Their make up leads directly into Wayne hatching the plan to defeat the Big Bad.
The Rugrats Movie: Phil, Lil and Chuckie abandon Tommy and Dil in the forest when the twins get sick and tired of Tommy constantly protecting Dil over them. In the twins' case, though, it may be more of With Friends Like These..., as they've been shown to abandon ship whenever things go wrong for them.
Noteably averted in the Bill and Ted movies—they don't have such a falling-out.

Literature

The Dark Tower: In the last book of the series, right before Roland is to meet up with The Crimson King and end his quest to find The Dark Tower, Susannah, the last human in his ka-tet to survive, decides to leave Roland citing his obsession with the tower and the quest over the health of his friends. Notable in that she doesn't come back to assist him at the last moment to help him defeat the Big Bad.
In Harry Potter and the Deathly Hallows, Ron and Harry argue over the lack of progress they're making in their quest, ultimately ending in Ron leaving the group. He eventually returns after destroying a Horcrux.

Live-Action TV

One Saved by the Bell episode featured Zack and Screech making a friendship bracelet business only to be upstaged by the rest of the Six-Student Clique, who were selling "Buddy Bands". Before the last commercial break, Screech quits (albeit after Zack, desperate for sales, gives Screech away as a "friend for an hour"), leaving Zack alone. This example is unusual in that it did not result in a The Power of Friendship moment, it instead resulted in Zack exacting revenge by destroying their business by buying a Buddy Band and giving it to the school principal, whose proud display of it makes it instantly unpopular to wear.

Western Animation

Discord breaks apart the friendship between the mane six in the 2-part premiere of the second season of My Little Pony: Friendship Is Magic. He cheats on this one; while he pretends that he's doing it via More Than Mind Control, it's quite clear that no, it isn't really more. He just gets kicks out of breaking them emotionally before brainwashing them to stop being friends.
Happened a lot in Trollz, usually because of Simon. Justified as their friendship was the key to defeating him.
"The Night Of The Living Burger," an episode of A Pup Named Scooby-Doo, starts off right away with Shaggy and Scooby on the outs. It was never made clear what they were arguing about, but they end up reconciling at the conclusion.
In Scooby-Doo! Mystery Incorporated, Scooby and Velma were on the outs with each other, quarreling over Shaggy for a time.