The player has just defeated The Dragon, or perhaps another servant of the Big Bad. While The Hero is quick to spare his enemy's life, he can take some satisfaction in knowing that he is, in fact, strong enough to take on the villainous forces that plague his world.
...at least until he finds out the truth.
You see, there was a reason why he won. This character was involved in some kind of plan, and part of the process required him to lose the battle. That's right! You're not as tough as you looked! Robbing you of the satisfaction of victory makes him just as much of a Magnificent Bastard as the fact that you have been unwittingly aiding his scheme!
...but wait. Something doesn't add up. His attacks were fierce. It took you a few tries to get past him, each time having to witness that dreaded Game Over screen when you failed. You know, if he's so interested in letting you win, maybe he could show enough courtesy to give you a bit more of an advantage in the battle?
True, if you won too easily, you might think that something's up. Or maybe he's so proud that he believes that if you failed to defeat him at merely a portion of his power, you don't deserve to be his unknowing pawn anyway.
Or maybe this is just Gameplay and Story Segregation. After all, there would be a lot of drama lost if you demonstrated that you were truly capable of destroying your enemies so early in the plot. Sure, a Hopeless Boss Fight would make a lot more sense, but where's the fun in that?
Most instances of this trope are also examples of The Battle Didn't Count, although for some villains, Death Is Just The Beginning...
Naturally, even reading the game names here is likely to be a SPOILER.
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Anime and Manga
Evangeline was the first villain in Mahou Sensei Negima!. Nearly three hundred chapters later she's still the most powerful character to appear. The entire first fight she was just playing around. At the end of the series she fights against Negi and Asuna together at their peak and is still winning.
In One Piece, Garp let Luffy win so he could save Ace, since Garp is a marine and Ace a pirate and his adopted grandson. His relation to Luffy was also a factor.
Garp's superior, Fleet Admiral Sengoku, isn't fooled for a second. But Garp is the legendary hero of the Marines, so there'd be too much bad PR if he were punished.
Heavily implied during Smoker's fight with Vergo. Smoker apparently let himself be beaten during the last seconds of their fight so that way Law could get his heart back. It's up to interpretation as to whether or not Smoker could have beaten Vergo on his own, because the only reason he let Law regain his heart was so that he would be out of debt to him.
In Naruto, this is stated to be the real reason why Sasuke could win against Itachi, who still completely dominated their fight and dropped dead right before he could finish the fight.
Subverted in Dragon Ball, where the world champion Hercule finds himself facing the fresh kid champion Trunks in a public fight. Having seen his battle with Goten earlier, Hercule realizes he has no chance whatsoever of winning the eight-year-old, so in order to save face, he pulls this off and pretends to have lost intentionally.
Exaggerated in the My Little Pony Friendship Is Magic fanfic Envy And Arrogance - When the mane six and their allies confront Arrogance in her sanctum and get completely trashed, she actually stops and expresses her annoyance with their weakness, outright stating that her boss' Xanatos Gambit had them beating her as the more favourable outcome. Then she purposefully launches into a long-winded Evil Gloating monologue, giving them the time to heal behind her back and prepare for round two. Then ,when it looks like they might actually stand a chance, she states that her job is done and disappears, willingly abandoning her host body.
Rainbooms and Royalty: When Twilight is fighting Blackened Armor (the brainwashed Shining Armor), he gloats about how he always beat her when they fought as foals. Twilight admits that he did always win... because even as a filly, she always held back with her magic out of fear of losing control and hurting somepony. Since she has no problem with that now, she proceeds to kick his ass and purify him.
The Ponies Of Olympus plays this for laughs: Iron Will gives Spike advice at how to beat him during their match in the preliminaries of the Atlas Strongest Tournament, so that when he does, he can try and offer to sell Spike his new book on fighting techniques.
The God Empress Of Ponykind: Tzeentch claims that he and the other Chaos Gods let the Emperor defeat them, faking their deaths in order to get rid of him.
In Diaries Of A Madman, Discord created the Elements of Harmony so that other species would stand a chance against him, as part of a way of breaking up the monotony of his endless existence.
In The Dresden FilesHarry wrests control of The Wild Hunt from the Erlking and Kringle, but he later realizes that there was no way he could have conceivably won that fight, and that they must have wanted him to lead the hunt, but couldn't just give it to him.
In the Discworld novel Maskerade, Granny Weatherwax plays a game of cards against Death for the life of a small child. If Granny wins, Death takes the soul of a cow instead. If Death wins, he gets the kid and Granny. Fortunately, this is the Discworld Death, who happens to be on the side of the living. Granny cheats and deals herself a better hand than Death, but he stops her, switches the cards... and then complains that he got "four ones" (read: four aces) resulting in a defeat. Rather an odd case of the trope since both characters were technically on the same side, but still.
Live Action Television
Television example: In an episode of Farscape, Rygel lets a villain win a chess-like game as part of a con.
Skip does this to Angel in season 3. It had something to do with the Jasmine arc in season 4, in which Skip was Jasmine's ally and Nigh Invulnerable, but is never fully explained.
Employed in Rutland Weekend Television, in which a prisoner who is going to be hanged tomorrow is playing chess against a guard, while another guard idly watches. The guard eventually says he's letting him win, to the prisoner's disbelief — both of the guards then reminisce about a time when he didn't let the prisoner win, effectively making him a Jerk Ass.
Playing Guard: I had this whole setup, could beat him in one move! But did I do it? No, I didn't!
Watching Guard: ...Well, you did.
Playing Guard: ...Yeh, I did. Beautiful move.
Watching Guard: Beat him in his last game'a chess...You Bastard.
Pretty much every boss fight in the first 75% of Metal Gear Solid. Some are more obvious about it than others; Vulcan Raven practically tells you that he let you win after you defeat him the first time. This group is incredibly devoted to this trope, as the majority of them die simply to convince you that you're not doing the dirty work for them. And was that Hind really necessary?
Other games in the series use this trope almost as much. Metal Gear Solid 3: Snake Eater even applies this trope to the final boss, kind of. (The Boss WANTS you to win, but she wasn't going to LET you win.)
Used again in MGS4, when Liquid at the end of the game fights Snake, it's pretty obvious that, having completed his agenda, he's just looking to go out with a bang. Which in this case means kicking Snake's ass a lot until Snake kills him.
After you defeat Death in Castlevania: Portrait of Ruin, he informs you that he has a reason to hold back. Indeed, he does: he can only bring back Dracula if you kill the guy who's usurping his power. This does not explain why he seizes you with chains and ends your life with one quickSinister Scythe swipe if you are unable to free yourself first.
After Soma fights Julius Belmont in Castlevania: Aria of Sorrow, he suspects something is up, as any other vampire hunter would have put up a better fight, and Julius admits he was holding back. Are highly damaging giant cross item crashes standard issue for vampire hunters now?
Near the beginning of the Ninja Gaiden X-Box remake, you fight Ryu's uncle and The Man Behind the Man Murai to a standstill. He calls it training, but during the fight never hesitates to kill you if you let him.
Devil May Cry 3 has the recurring boss and/or advisor, Jester, who claims he needs Dante alive but doesn't hold back. Given that Jester was only a boss in the "Special Edition", which was somewhat panned for its quality, it is difficult to say if this trope occurs intentionally or out of developer laziness. He's actually Arkham.
In Mega Man X 5, the first boss fight is against Sigma in the form of a large floating head. After the player defeats him, a virus breaks through Earth, which was what he wanted. Zero clearly states "he lost to us on purpose!"
Tales of Eternia, about halfway through the game, the temporary party member Ras reveals that he's the incredibly powerful knight you've been hearing about, and attacks you to prevent you from escaping to Celestia. After you beat him to a pulp and get to the next town, your party realizes that he couldn't have been fighting you for real - he kept pulling his punches and not taking advantage of openings, leading them to conclude that he let them win.
Inverted in Dawn of the New World, where In order to get the good ending, Emil has to let Lloyd and Marta win. Unfortunately, You're playing as Emil in that fight, so that means YOU have to throw the fight. Beating them gives you the Bad Ending.
Translation: During that climactic battle in Path of Radiance, Ike reveals that his father crippled his sword arm, a fact that the Black Knight didn't know. As the Black Knight's true goals was to surpass his teacher, aka Ike's father, this revelation makes the Black Knight realize that his victory over Ike's father was hollow, as he never got to experience Greil's true ability. So he allows Ike to win in the hopes that later Ike would become as powerful and skilled as Greil, in short a substitute for Greil to test his skills against.
Original: The Black Knight's warp powder malfunctioned, leaving Ike to fight his spirit, that was not only weaker then his true self, but returned to his body after defeat.
Almost: it was entirely irrelevant to the Daemon who won, as either way there would lots of killing to power its release. After all, Khorne cares not from whom the blood flows, only that it does.
Thunder Force V has you battling the Guardian, an AI infested with alien coding (from the ship of the previous game). Towards the end, however, it's revealed that Guardian was helping the pilot all along. Since it couldn't destroy itself, it deliberately paved a path for the pilot.
Warcraft III begins with a nice example of this in the Human Campaign with The Lich King tricking Arthas into picking up a BFS and becoming his champion/bitch.
The Lich King, now Arthas himself, continues to do this in World of Warcraft. A good number of times players defeat his lieutenants and wipe out large numbers of his soldiers. In the final battle, Arthas reveals that it was all a plan to get them stronger, to let them become the champions of the world... so that he could kill them all in one shot and raise them as undead. He would have succeeded, too, if the ghost of Arthas's father didn't revive everyone at the last moment.
In Mega Man Zero 4, The Dragon Kraft is apparently going along with the Big Bad's evil schemes because he's descended into a "survival is everything" paradigm and thinks it's the only way to protect his and his ex's skin. After the first battle against Kraft, Zero asks him what's holding him back. Later, Kraft pulls a (sorta) Heel-Face Turn into a Knight Templar and threatens to Kill Sat an entire city of civilians to get at the Big Bad, and you have to go stop him. This time, he believes in what he's fighting for, so naturally, he's harder.
Subverted in Kingdom Hearts: Chain of Memories; after the first fight with Larxene, she is seen in a later cutscene musing about how it was hard to hold back enough to throw the fight - but then Axel and Vexen both mock her for trying to justify getting her ass kicked, even though what she claimed was true as evidenced by her second fight with the key bearer. Axel's hypocrisy isn't lost in the gamer as he also let Sora win in his first match. Vexen just seems to despise Larx due to her association with "that dog Marluxia", so he probably didn't want to miss the chance of making fun of her.
Vexen also holds back against Sora the first time in order to get data on him and create the Twilight Town card.
In Reverse/Rebirth, Axel tells Zexion that even in the second fight, he decided to let Sora think that he'd finished him off.
In EverQuest II the resident Lord of all Vampires, Mayong Mistmoore, reveals to players at the end of the major Rise of Kunark questline that he's the God of Blood, and he allowed the ancient and powerful sword SoulFire to be taken from him simply because he finished studying it. He then promptly begins studying another ancient artifact, a doomsday calendar called the 'Chelsith Stone'. (One must wonder about the impact of letting an ancient and powerful Vampire/God study equally ancient and powerful artifacts).
In Baldur's Gate 2, Kangaxx is a disembodied lich, whose body was torn apart, its bits hidden in tombs. If you reunite his body for him, he rewards you (or attempts to) with death. If he fails, he laughs madly, as he apparently needed to get his body back first, then have it destroyed, to be transformed into a demi-lich, which is much harder to kill and much more likely to ruin your day.
The campaign mode for Naruto: Ultimate Ninja 3 makes heavy use of this trope. In order for the story to advance, Naruto has to defeat most of the other Leaf ninja in single combat, including adult chunin and jonin who are canonically stronger and much more skilled than he is. However, since the competition is a friendly one and Naruto has more emotionally invested in it than they do, the battles with stronger ninja such as Shizune, Anko, and Kakashi tend to end with Naruto absolutely exhausted and the stronger ninja saying "Okay, that was pretty good, you obviously care more about this than I do, so here are my Plot Coupons," having not even broken a sweat.
At the end of the campaign, Kakashi defeats Naruto, then forfeits the match, claiming Naruto won.
Used contstantly in many of the Touhou games, partially because most denizens of Gensokyo view fighting as a game and mostly to justify defeating some of the most absurdly powerful beings imaginable (manipulation of fate, manipulation of boundaries, killing anyone with a thought, control of nuclear fusion etcetera). Explicitly stated in Subterranean Animism, in which the stage 3 boss Yuugi says she was just playing around, her sake NOT EVEN DROP!
Surprisingly used after beating the Penultimateboss of Bayonetta.
In Suikoden I, if Pahn wins his duel against Teo (which is ridiculously hard to do unless you've done some serious level grinding), he will wonder aloud if Teo went easy on him in the aftermath of the battle.
And Suikoden II features an inversion in that it requires you to let Jowy mortally wound you in an optional battle at the very end of the game to get the best ending. Luckily, you get better.
Mild example in the form of Slayer in any battle. His story dialogue and battle animations suggest a strength far greater than most of the cast, and his defeat pose has him simply lying down with an "I'm tired of this" look as opposed to being knocked out like everyone else. Especially evident in stories where he fights Sol Badguy, arguably the strongest person in the GG universe next to Slayer.
In Super Paper Mario, Mr. L claims that he was scouting the heroes, and he was a ridiculously strong boss (his attacks do more damage than anything else likely to hit you until you reach Count Bleck) for that particular part of the game. Considering Luigi's abilities in other games, he's probably telling the truth.
At the end of chapter 6 in Duel Savior Destiny you finally get the change to have a fight with Lily. After winning, she mutters about how she was intending to do this but in the end actually fought seriously.
In Project × Zone, Sanger declares that he lets Yuri and Estelle win, otherwise he could have dealt a fatal blow against them. Considering you're using Yuri and Estelle at this point in a very short two-on-one duel, you would have to use an item just to survive against him and that Sanger's comments may be directed more to the player.
Bravely Default: This unintentionally happens after the first fight with Victoria and Victor. Right as they are about to finish the heroes off, Victoria suffers a sudden and violent seizure, forcing Victor to call the battle off.
Spoofed in South Park. Satan challenged Jesus to fight for the fate of the world. It was a scam. Satan knew everyone would bet on him, given how strong he was compared to Jesus (this was before he turned Badass in "Red Sleigh Down"), so Satan bet on Jesus and threw the match, returning to hell with all the money.
Jimbo Kern: Man! That guy is a jerk!
In Home Movies, Brendan decides to get own back on his bully, Shannon and has Melissa film a rematch to the fight. Shannon coincidentally tries to apologize for beating him up, and while Brendan pretends to accept it, he sucker punches him in the stomach. As Shannon appears to be near tears and reeling in pain, Brendan begins to dance over his victory, not noticing Shannon by then already got up and told Melissa he was faking it and did it to give him some of pride in standing up to him.