Mysterious Backer

More often than not when a story has a Big Bad there will be a Big Good to counter them. This has a number of advantages; it keeps the heroes' side balanced against the antagonists', provides a source of support for the heroes and generally stops the series getting too cynical. On the other hand, it raises some problems. Namely, with the strength of such a strong ally, where's the tension? The Big Good could easily end up being a Game Breaker, which also begs the question of why they don't get off their arse and send their villainous counterpart packing (or vice versa).

Cue this trope - a powerful benefactor of the heroes (essentially doing the same thing in the story that a Big Good would) who has their own agenda or reasons for helping them. Perhaps they're mysterious and hard to trust, perhaps they're visible, but seem a little too keen to Shoot the Dog. Other times, they're genuinely benevolent beings who are working within some sort of non-interference clause, and may employ the same tactics as their opponents. Either way, they'll provide the support the cast needs, but the heroes (or at least the audience) don't quite know if they can be trusted. Even if they are the Big Good proper, they might not be planning to do things in an entirely moral manner or have it in for the heroes and wish to make them suffer more than they really need to. In a worst case scenario, they might become the new Big Bad.

Remember that this isn't a simple case of Omniscient Morality License or In Mysterious Ways, nor are they a Big Good who likes to stay hidden or keep an air of mystery around themselves; the entity in question must be at least visibly untrustworthy rather than having an excuse for their seemingly questionable behaviour. A hero with this trope as their main support might (but doesn't always) find themselves as an Unwitting Pawn, although to count as this trope, the Mysterious Backer must further the heroes' agenda as much as their own (assuming they aren't one and the same).

A subtrope of The Powers That Be.

See Poisonous Friend for another type of ally who might not see eye to eye with the rest of the team. Compare Anonymous Benefactor and Mysterious Employer, two similar but subtly different types of patrons. Contrast with Big Bad Friend, for someone who's close to and trusted by the hero, but leads the villains and Enigmatic Minion, for someone on the villain's side with unclear motives.

Examples of Mysterious Backer include:

Anime and Manga

In Puella Magi Madoka Magica, Kyube is this to the letter. even after finishing the series, his Blue and Orange Morality makes it difficult to discern whether or not he was a villain or hero, or any variation involving the prefix "anti-".
Urahara from Bleach. He guides Ichigo through the whole series, and obviously knows more than just about anyone else when it comes to just what the hell is going on, but don't expect him to fill you in any time soon.
In Suzumiya Haruhi, the Data Entity fits this role.
Professor Oak, from Pokemon. No, seriously. Think about it. Almost nothing has been revealed about his past, just that he's a Pokemon Professor and mentor to Red and Blue in the original game. The anime doesn't tell much about his past either, despite him being practically a regular. In fact, more than a few fans were surprised that he had actually trained a Dragonite!
With that in mind, Shanks from One Piece is similar to Professor Oak. What do we know about him? Well, he's powerful, influential (enough for everyone to stand up and take notice when he shows up), is one of the few remaining members of the Roger Pirates, and is a friend and ally of the protagonist. Other than that, not so much.
- By the same factor, Silvers Raliegh, another member of Roger's crew. Slightly more is known about him, but all the heroes truly know is that they can trust him.
Tsukikage Fuma from Yu-Gi-Oh! ARC-V (called Moon Shadow in the dub) is the most mysterious member of the Lancers, the team of teenagers with attitudes recruited by Declan for the multi-dimensional conflict. Initially Declan's bodyguard (meaning Declan himself likely knows more about him than anyone else does) he seems to have little history other than that, although he does seem to form close connections to the others. But still, the only thing most of them really know about Fuma is, he's on their side. Of course, he is a Ninja, and not the "highly visible" type.

Comic Books

Green Lantern‍'‍s Guardians of the Universe. They think they're the Big Good, but they're completely full of themselves and wind up being the cause of a lot of messes the Lanterns have to clean up.
Invoked in the second series of Runaways. A group of former superheroes get a mysterious phone call asking them to come out of retirement for One Last Job. The heroes call him out, but they still wind up taking the job.
Most of the major Marvel principalities, particularly the Vishanti. They're mainly on the side of good, but they have a perspective which is sometimes completely alien to normal humans. On more than one occasion Doctor Strange has renounced them, taking the loss of power as a consequence, rather than be beholden to them any longer.

Film

In the Star Wars prequel trilogy Senator Palpatine fulfills this role, since he's apparently helping the protagonists, but anyone who had already seen the original trilogy knew what he had in mind.
Rufus in Bill & Ted's Excellent Adventure. Neither the two protagonists nor the viewers know why he's helping them until he tells them at the very end.
- He fits the Trope in the sequel too, as not even the viewers know until the end that the — female — concert director who gives the protagonists a chance is actually him in disguise.
Deep Throat in All the President's Men, emphasis on "mysterious". Of course, he was based on an informant whose identity and motives were, at the time, a heavily-guarded secret, but the film certainly upped the mysterious part, portraying him as a shadowy figure with a gravely voice. Very much unlike the actual Mark Felt, especially when he admitted, publicly, to being the informant in 2005.
The Driver in Drive. It's not revealed who he is, what his relation is to the woman and child he's escorting, or just why he's protecting them; some scenes even shed doubt on whether he's there at all. Important thing is, he is there, and he is helping them.

Literature

The Dresden Files has loads of these; Marcone (a pragmatic, but still ruthless, gangster), the head of the White Council (who is the Big Good...but also has it in for Harry), pretty much any fey that helps him (since Blue and Orange Morality is their chief export).
The Ellimist from Animorphs technically tries to help the heroes, but he is either too roundabout in his methods to really gain their trust or too held up by Crayak (with whom he has a self-enforced stalemate) to help at all.
Eru in all of J. R. R. Tolkien's works. All of the Valar as well.
Melisandre from A Song of Ice and Fire. A red priestess from Asshai who supports and advises Lord Stannis Baratheon in his campaign for the throne of Westeros and believes he is The Chosen One. It's ambiguous whether she's actually good; she might be a Tautological Templar.

Live-Action TV

Warehouse 13 (which has its own series) serve as this in Eureka.
The Vorlons were this in the first part of Babylon 5. Their definition of good (as opposed to the chaos of the Shadows) lets them help the heroes, but they go past good. Soon they are blowing stuff up veering into Lawful Stupid territory.
Zordon, from Mighty Morphin Power Rangers and the next three series in the franchise. Yeah, he's clearly on the good guys' side and is a font of ancient wisdom but... How much do we know about his past and motivations? Very, very little, in fact.

Video Games

Corak from the first five games in the Might and Magic franchise is even called "Corak the Mysterious" to any who know of him. The player characters in each game are pretty much following the directives of an unseen figure named Corak who doesn't reveal his purpose until the end, that he is an android built by the Ancients to apprehend Sheltem, a similar, malfunctioning android with genocidal goals.
Mantarok from Eternal Darkness. Sure it's the only one of the ancients who isn't planning to enter the world and run amok, is activally opposing the others and even spent some time serving as a small village's personal fertility god. On the other hand, it's hardly in a position to oppose humanity and after masterminding the destruction of the other three ancients, who knows what it's planning...
- Word of God also states that another ancient is responsible for protecting humans by cleaning away the remains of Eldritch Abominations (as seen in the form of the yellow glow that accompanies the disappearing dead enemies), and may be an example of this (its yellow element certainly blocks Alex's progress in the final chapter).
Sammael from Darksiders; An archdemon from hell so Powerful that the destroyer had him imprisoned and reduced to an extra. But He uses what power he does have left to help War, the games protagonist, so that War will help him get his powers back (and because he respects a man bent on revenge).
Guild Wars: The Order of Whispers, in Nightfall, is the Big Good organization confronting Abaddon. However, they're a very mysterious lot, none more so than the Master of Whispers himself (one of the NPC heroes the player can acquire during the campaign), and the player character lampshades this in in-game dialogue with the Order of Whispers shrine attendants from which he/she gets bonuses in explorable areas, saying, in almost as many words, "I don't trust you or your Order, but we have a common enemy, so I'll help you."
Verus in Baten Kaitos Origins, detailed on the game's character page.
Theresa in Fable 2 is textbook this trope—apparently the Big Good of the whole game until the last ten seconds of the final Cutscene.
In Mass Effect 2, despite the nature of the organization, Cerberus acts like this towards Shepard.
Tales of Monkey Island portrays the Voodoo Lady that has helped Guybrush throughout his career as this.
Zeno Clash has Golem; a mysterious giant with a face that's shrouded in shadow and an extremely out of place Rubix cube. He seems to know exactly what's going on, is opposing Father-Mother and guide's Ghat...but seriously, what the hell are his goals? Not to mention he seems to be subordinate to a Mysterious Watcher of some sort.
In Final Fantasy Tactics, Delita effectively acts as one for Ramza. Delita's biggest contribution for Ramza's cause is effectively deploying Thunder God Cid to fight along his side. Talk about friends in high places...
Zoe from Resident Evil 7: Biohazard. For most of the game, she is a voice on the phone directing and advising Ethan. It is not revealed until the end that she is a member of the Baker family who has managed to resist being enslaved by Eveline's mind control and survived by pretending she had succumbed to it.
- "The Duke" from Resident Evil Village. He's a lot like the Merchant from Resident Evil 4, but he helps Ethan in a few plot-related ways.
  - Subverted, however, with the mysterious old woman in the same game. She appears to help Ethan, but she is actually the Big Bad in disguise.
The Mysterious Stranger in the Fallout games. This is a perk (sort of like a skill) you can get in all of the games except the first. If you have it, the aptly named Mysterious Stranger - a guy with a trenchcoat and fedora, smoking a cigarette and packing heat - will appear randomly (his appearance heralded by a cool guitar riff) to help you in battles. Who is he? Nobody knows, he's just so mysterious.
In Pokemon Legends: Arceus, there is, well, Arceus. It doesn't say why it wants the player to "seek out all Pokémon", or why it wants you to do so, it just tells you to do so - of course, Arceus is the God of Pokemon, and as such, moves In Mysterious Ways.

Web Original

Red vs. Blue has the enigmatic Director, head of Project Freelancer.
- Vic too in the early episodes, in the sense of being Mission Control with some sort of agenda.

Real Life

In the late thirties, before the organizing of the OSS, it was known for American intelligence to be conducted by sending a personal protégé of the POTUS or some other powerful figure to look into matters in an almost pulpish adventure. This had mixed results to say the least, but if the figure chosen had other connections (like being an Old Whatever-this-particular-country Hand), it might prove useful and in any case the representative had the direct ear of the backer. Several celebrities were rumored to have done so, as well as some people who actually became intelligence professionals like "Wild Bill" Donovan (who had previously gained notability in an occupation less honest then espionage).
As previously stated, the Watergate informant (often referred to as "Deep Throat") who provided information to Washington Post reporters Bob Woodward and Carl Bernstein was this for a long time. His identity was a secret known only to them, and they swore they would not reveal it until his death. For years, news agencies and other organizations could only propose theories as to his identity and motivation — some outright refused to believe he existed, given how suspiciously convenient of a figure he was. It wasn't until 2005 that Deep Throat was revealed to be FBI Associate Director Mark Felt, who came forward on his own. He was, in fact, always the administration's main suspect, given the nature of the information he was doling out, so it's less of a revelation than it looks on the surface.