The Handler

A character type in Spy Fiction, particularly in those which lean in the Government Conspiracy direction and/or those with assassins as their protagonists. The heroes don't have access to their bosses, but instead have orders relayed to them through the "Handler" whose jobs include looking out for the hero's physical and emotional well-being and/or killing the hero should they act out of line. In cases with the hero and Handler being of different genders, it is somewhat common for the Handler to have Unresolved Sexual Tension with the hero as they are the "human face" of the secret organization to which the hero belongs.

Examples of The Handler include:

Anime and Manga

Darker than Black has the abrasive Jerk with a Heart of Gold Huang relaying orders to Hei, the Anti-Hero of the series
- Who in turn has another higher ranked Handler... who just so happens to be a Contractor. The Syndicate's cell structure is somewhat odd at times.
All of the girls of Gunslinger Girl get one, and relationship dynamics vary with each one: they can be either the sweetest guys (like Giuseppe until he Took a Level in Jerkass) or the biggest jerkasses (like Jean who doing it to toughen himself and detaches him from her and Lauro who DIES for that).
Weiss in Weiss Kreuz go through several of these: Manx, Birman, Botan, and Rex. Their mortality rate isn't much better than that of anyone else who comes into contact with Weiss.
In Claymore, the handlers of the titular characters (particularly Louvre) are a major feature of the plot.
Mr. Kim in the anime R.O.D the TV, to the Paper Sisters when they do contract work for Dokusensha. He's described exactly as a handler several times.
Watari is considered L's handler from Death Note - the name "Watari" was chosen because it means handler.
In Maiden Rose, Klaus has one in Taki's country, who supplies him with drugs among other things. When he tells Klaus he's getting out soon and Klaus should too before he dies there Klaus mocks him for getting too attached to him.
Fullmetal Alchemist has a rank-reversed version. Colonel Roy Mustang appoints his second-in-command, Lieutenant Riza Hawkeye, to be his handler. He has even ordered her, should he ever undergo a Face Heel Turn, to kill him on the spot.

Comic Books

Frank's only real connection to the world in RED is his handler, Sally. The equivalent character in the movie isn't an example, as for various reasons her role was both changed and expanded.

Film

Sidney was the title character's handler in John Woo's The Killer, who acted as a Blood Brother to him.
Nicky Parsons of the Bourne movies fits this trope word for word.
Tom Hagen was The Godfather's adopted son and personal assistant or consigliori.

Literature

In the Quiller novels by Adam Hall each Bureau "shadow executive" has a director-in-the-field who organises safehouses, communication, transport, identity papers, liaison with government officials—in short, anything the agent needs for the mission; especially since Bureau agents are never told what the mission is about, the idea being that the agent should not get distracted by any larger political implications. Agents have a right to refuse to work with a particular director, given that trust between the two is so important. Quiller's preferred director is Ferris, even though he's slightly creepy (he's rumored to strangle mice).
Due to its small size, a common methodology of Special Circumstances from The Culture novels is to employ or manipulate non-SC or even non-Culture agents to do the dirty work, with SC operatives acting as handlers. Examples include Diziet Sma in Use Of Weapons and Flere-Imsaho in The Player Of Games.
Andrew Osnard (played by Pierce Brosnan in the film) of John Le Carré's The Tailor of Panama is a classic example, recruiting title character Harold Pendel (Geoffrey Rush) as a spy and applying so much pressure to him that he makes up information that when acted on majorly destabilises the region
- Ned, from Le Carré's The Russia House and The Secret Pilgrim.
- Actually practically all of Le Carre's spy novels include some sort of handler.
CIA department head Bill Carstairs is this for Emily Pollifax in Dorothy Gilman's Mrs. Pollifax novels.

Live Action TV

In Chuck, Sarah and Casey serve as Handlers for the title character
The Invisible Man TV series had Claire the "Keeper"
She Spies. The title characters had two Agent Handlers in the course of the show.
Michael (or Bob in the movie) filled the same role for La Femme Nikita, and in the case of the former, there was definite UST.
Bosley of Charlie's Angels in both the TV show and films.
Carla in Burn Notice
- Victor is specifically called this
Michael Vaughn served as the Case Officer for Sydney Bristow.
Boyd, then later Paul, is Echo's handler in Dollhouse.
Wiseguy. Frank McPike, Vinnie Terranova's Deadpan Snarker boss in the Organised Crime Bureau.
In Scarecrow and Mrs. King, Scarecrow is in some ways more like a handler then a partner. At the least if a veteran agent ever worked with a housewife turned spy (actually not impossible in Real Life though it would probably be less Hallmark-like) he would probably be a handler even if he told her he was a partner. In this case both the handler and the handled are heroic characters.
In The Dresden Files, Ebenezer McCoy was assigned as a troubled teenage Harry's handler (unbeknownst to Harry) in case he ever went nuts and needed to be eliminated.
Peter to Neal in White Collar
Mr. Morden in Babylon 5
Now and Again: Dr. Morris was Michael Wiseman's handler and keeper, tasked with both setting up Michael's missions and preventing him from interacting with the outside world (especially his widow).
Buffy the Vampire Slayer. In theory, the Watcher plays this role for the Slayer. Whether Buffy or Faith chose to follow the Watchers Council's orders is another matter.

Video Games

Diana filled this role for 47 in Hitman Blood Money.
Any shadowy government types who serve as quest-givers in a GTA game, notably Mike Toreno in San Andreas, and "United Liberty Paper" in Grand Theft Auto 4.
Alpha Protocol takes this Up to Eleven; there are eight handlers used throughout the various missions. And yes, Mike and his primary (female) handler Mina have Unresolved Sexual Tension.
- Mike can have UST with all four of the potential female handlers, if you play your cards right with the dialogue options.
Admiral Steven Hackett in Mass Effect serves as the face and voice of the Alliance Navy for the audience and is Shepard's primary contact in the Alliance command. In Mass Effect 2, Miranda arguably takes on this role, though Shepard spends rather more time tending to her emotional well-being than she does to Shepard's. There is also way more sexual tension in the second case than in the first.

Real Life

In Real Life these people are known as Agent Handlers or Case Officers