The right-hand man of The Leader, or second in command. Usually The Lancer and a Foil. The one who takes over the "ship" when The Captain wants to be off doing non-Captainy things.
Often called simply Number Two (or, confusingly, Number One), although terms like First Mate or Executive Officer frequently appear in military fiction especially involving the chain of command in a Command Roster. Compare The Lancer in the Five-Man Band, who is usually not too happy about that. Although sometimes the Number Two is also The Lancer to provide a contrast between authority figures. In-universe this is also a good idea: If The Leader is Hot-Blooded then he needs The Stoic to balance him, and vice versa.
Strictly, in the Royal Navy, at least, the Captain would have an Executive Officer and a First Lieutenant, both ranks being held by a single person on smaller ships. Hence the XO (also known as Number One or sometimes "the Jimmy" ) would be the captain's Right Hand Man and Number Two would be his immediate junior. The position also goes by the title Executive Officer (XO), particularly in the American military.
If the creators did the research, the (XO) is much more likely to interact with the crew. On a ship, "Number One" is responsible for the crew: training, ordinary discipline (that is motivating the NCOs to motivate the others) setting watches for the officers etc. The Captain's job is to decide what the ship should do, Number Two makes sure the ship and crew can do it. A Captain Smooth and Sergeant Rough situation can result from this.
If the Number Two is also the Big Bad's main fighter, then he's The Dragon. Sometimes gets "promoted" to Commander Contrarian. The dimwit version is Number Two for Brains.
Not to be confused with the original script for Back to the Future Part II. Or the euphemism for solid waste.
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Anime and Manga
Yu-Gi-Oh! GX: Rivals Judai's and Misawa's nicknames for each other are "Number 1" and "Number 2".
In Sonic X, Tails is often seen leading the other characters during Sonic's absence. Sonic also refers to Tails as My Right hand man!
Fuyutsuki plays this role in Neon Genesis Evangelion, typically being left in charge at the drop of a hat (or an Angel) and it's notably rare for both himself and Commander Ikari to be absent (almost as notable as it is for Ikari to be present).
Zoro from One Piece is this, whenever Luffy isn't around. Nami sometimes is this too.
And from other pirate groups, we have Marco, who is this to Whitebeard. Silvers Rayleigh to Gold Roger. Brook was like this to his previous captain, before circumstances forced him into becoming Captain himself. Killer to Kid. Every other first mate counts.
Nico Robin to Crocodile, as well.
During the Dressrosa Arc, it is revealed that Sabo, who was thought to be dead is this for the Revolutionary Army.
Zetsu is Number Two for Uchiha Madara in the Akatsuki.
Konan for Nagato in Amegakure.
In the backstory, Uchiha Madara was the First Hokage's Number Two. Unfortunately for the rest of the world, he developed an Inferiority Superiority Complex towards his former friend.
Fullmetal Alchemist, being a very military-based storyline, has these in different places. Most evident to the reader/viewer, Riza Hawkeye is the second-in-command of Roy Mustang's unit.
Casca was this to Griffith in Berserk, and took over leadership of the Band of the Hawk following Griffith's imprisonment by the King (which came about because Griffith had sex with Princess Charlotte following the departure of his greatest warrior, Guts).
Gundam SEED: Murrue Ramius had Natarle Badgiruel (before they were split up by the top brass). In Gundam SEED Destiny Ramius has Andrew Waldfeld, Talia Gladys has Arthur Trine, Yzak Joule has Dearka Elsman, and Neo Roanoke has Ian Lee.
In Legend of Galactic Heroes, Siegfried Kircheis effectively serve this role to Reinhard von Lohengramm. Most of Reinhard's subordinates recognise and accept this disposition, except for Paul von Oberstein, who believes that The Leader should not have a Number Two as that may lead to the creation of an alternate power base.
Bleach: The Gotei 13 is split into 13 divisions. Each division is a semi-autonomous unit that is controlled by The Captain and backed up by the Lieutenant. In the absence of a captain, the Lieutenant has to shoulder full responsibility for the division.
Levi from Attack on Titan is this to Commander Erwin, who is one of the few people Levi respects. Though that doesn't exempt Erwin from Levi's rudeness.
In the Fantastic Four, Sue was always more or less Reed's Number Two, but it was a role she rarely had to play. Then Reed was killed off for a couple of years, and during that time, Sue had to step up to become team leader. This became a part of her personality and changed the team dynamic a bit. Reed still calls the shots (and Sue prefers it that way), but when he's absent, she'll easily take charge.
In Sonic the Comic the role of Number Two is taken by Amy Rose she leads the Freedom Fighters when Sonic is unable to (i.e. Sonic has tured into Super Sonic or Sonic is trapped in the Special Zone).
Hound is this to Jazz in Transformers Meta and leads the group when the latter is incapable of doing so.
He tried to once, but it didn't exactly go well and Wheeljack ended up saving the day.
In the Austin Powers series, Dr. Evil's Number Two was indeed called Number Two, not only as a rank but as being his proper name as well (IE: he's Mr. Two). To further drive the joke down, Number Two once gained his OWN Number Two, which, of course was deemed "Number Three". To further the irony, this Number Three later turned out to be The Mole for the Good Guys, who was only referred to as "The Mole" even though he had a recurring role in the movie.
Used for a quick gag in the first and third movies, the first calling out the Toilet Humor version, the second using it for school testing results.
In the film Meet Dave, the Number Two of The Captain was also literally named Number Two (or sometimes simply 'Two'), and is given no other name. He becomes concerned about the Captain's lack of enthusiasm for the ship's mission, especially his treating of humans as equals, and ultimately pulls an Anti-Mutiny.
Herc Hansen to Stacker Pentecost in Pacific Rim. It makes sense seeing how both of them were involved in the Jaeger program when it first began and piloted Mark-1 Jaegers and were likely good friends. Taken further when after Pentecost's Heroic Sacrifice, Herc becomes the new Marshall.
For most of the Harry Potter series, Professor McGonagall is Dumbledore's Number Two, holding the title of "deputy headmistress".
That's relating to the school and the students. For the Order of the Phoenix, Dumbledore's Number Two is Mad-Eye Moody. For protecting Harry and gathering intel on Voldemort, Snape is his Number Two. And for facing down Voldemort and his allies, Harry ends up in this position. Really, Dumbledore's got these all over the place.
In the Hand of Thrawn Duology, General Bel Iblis strikes a deal with Booster Terrik - Booster's Star Destroyer gets fixed up and flies for the New Republic in her time of need, and Booster gets to keep captaining her during this. When they fly into battle against hopeless odds and Booster wants to save his ship, Bel Iblis overrides him. Booster angrily reminds him that he's the captain of this ship. Bel Iblis calmly says yes. But he is the ship's admiral.
In the X-Wing Series, although Wedge heads both squadrons he also has a second. Tycho seems to fill the role in Rogue Squadron, at least after those murder and treason charges were cleared up, and Face has the job in Wraith Squadron.
Bean to Ender: if Ender ever broke under the strain, the plan was to have Bean take over. His own portrayal of the same story has him deciding that while he is the better tactician, he is not a commander of men and thus should be in such a role.
Subverted in Thunderball: the senior people of SPECTRE are addressed by code numbers such as "Number Two" during their meetings, but the number assigned to each person changes on a monthly rotation. Blofeld, absolute leader of SPECTRE, was "Number Two" in that book. (The movie made Blofeld Number One to avoid confusing viewers about who was in charge, since it didn't have the narrative explaining that this was a security measure.)
In Warrior Cats, all leaders appoint a "deputy", who is the second in command and succeeds them when they die. Both leader and deputy have quite a bit of responsibility, with the deputy doing jobs such as organizing all patrols.
The Cruel Sea covers a "Number One's" duties (on anti-submarine craft) in exhaustive detail, since the protagonist is one (and the writer WAS one).
Tobias to Jake in Animorphs as Jake also usually appoints him leader of the Marco-Tobias-Ax sub-team, which ended up carrying the end of the war.
Song at Dawn: Dragonetz has three of them: Arnaud for the battlefield, Al-Hisba for the paper mill and Sanchez in spying.
In Gifts, Brantor Canoc of Caspromant has Alloc. Alloc considers himself not nearly as smart as Canoc or heir Orrec and his gift is not as strong, but he's solid and sensible. When Canoc dies and Orrec 'inherits', Alloc still considers himself to be the Number Two even though Orrec is mostly just agreeing with his suggestions.
William Bush through most of the Horatio Hornblower books, as his first lieutenant and then the captain of Commodore Hornblower's flagship. He's The Lancer: not a genius like Hornblower, but solid, steady, and uncomplicated. He's frequently shown to e an excellent sailor who can always carry through Hornblower's plans reliably (and tries, if he can, to make sure Hornblower actually eats and sleeps).
In the Jacobs Ladder Trilogy Tristen is this to Perceval in the second volume, calling himself First Mate and acting the part.
Live Action TV
Spock is Kirk's Number Two on Star Trek: The Original Series, and Riker is Picard's Number Two on The Next Generation. Though he, and other Star Trek seconds-in-command, are referred to as "Number One", this is because their title is First Officer (i.e., the number one ranking officer after the captain). They're still second in command. As we see (such as in the original Lower Deck Episode, "Lower Decks"), aboard Starfleet vessels the first officer is very much the authority figure to the crew: setting watch schedules, disciplining the crew, et cetera.
In one episode of TNG, "Conundrum", the crew had their memories altered by an energy pulse, while at the same time the alien responsible took on human form and transported onboard the Enterprise. According to the temporary External Retcon, the alien was Commander MacDuff, First Officer, second-in-command, and "Number One" as Picard called him. Meanwhile, Riker, though he had the same rank, was Second Officer.
In another TNG episode, Q derisively refers to Riker as "Number Two."
In the first Pilot of the original series The Cage/The Menagerie, Majel Barrett played Captain Pike's cold emotionless "Number One", who was referred to by no other name. Some didn't like the actress, or the idea of a woman in authority, so the character was dropped for the second pilot and series, and her unemotional nature was added to Spock's characterisation. (Gene Roddenberry snuck the actress, Majel Barrett—his girlfriend and later wife—back into the series later in a blonde wig as Nurse Chapel, a safely traditional and subordinate female role.)
An episode of Star Trek: TNG has Riker participate in an officer exchange program with the Klingons. He is temporarily assigned as the First Officer of the IKS Pagh under Captain Kargan, with Lieutenant Klag, the usual First Officer being temporarily his second. While preparing for the transfer, he quizzes Worf on Klingon customs and fleet regulations. He is surprised to learn that one of the duties of the First Officer is to kill his captain if he proves himself incompetent and take command (there's a reason the related trope is called the Klingon Promotion), which is why every Klingon officer carries a d'k tahg (dagger). A later episode has Kurn come aboard the Enterprise to do the same (and meet his brother Worf for the first time).
Leo McGarry on The West Wing, the President's Chief-Of-Staff. Since Vice-Presidents are only used as a political tactic in the U.S., they usually don't actually have much to do with running the country, and in practice, the only thing that makes Leo a slight subversion of the Number Two is that he can't ascend to President upon death or disability. Legally and in public, that is...
This leads to a few problems in season 2: when the President is shot and rushed into surgery everyone reflexively takes their orders from Leo until Bartlet's concious again. Then the dust settles and people start pointing out that, legally speaking, they can't do that.
Toby: The Commander in Chief had just been attacked, he was under a general anesthetic, a fugitive was at large, the manhunt included every federal state and local law enforcement agency. The Virginia, Maryland, New Jersey, Pennsylvania and Delaware National Guard units were federalized. The KH-10s showed Republican Guard movement in southern Iraq. And 12 hours earlier an F-117 was shot down in the no-fly, and the Vice President's authority was murky at best! The National Security Advisor and the Secretary of State didn't know who they were taking their orders from. I wasn't in the Situation Room that night, but I'll bet all the money in my pockets against all the money in your pockets that it was Leo. Who no one elected! For 90 minutes that night, there was a coup d'état in this country.
Josh eventually becomes Number Two to Matt Santos.
The Office (U.S. version) has several of these. Jan from the executive branch has Michael (the manager) and Toby (the HR liaison) as her Number Twos. Dwight acts as Michael's Number Two but is not in any official way. Jim is his actual Number Two by season 3, although what with how much work Michael actually gets done, Jim is the one actually running the office.
In LOST Ben becomes this to Hurley after he becomes protector of The Island in the Grand Finale
In The Prisoner, The Village is for most intents and purposes run by Number Two, although the individual holding this title changes frequently. This of course raises the inevitable question, "Who is Number One?" The subsequent Prisonergraphic novel "Shattered Visage" answers this with another question: "does the existence of Number Two imply the existence of Number One?"
Zoe is Mal's Number Two in Firefly. Mal was Zoe's superior back when they were still in the war, and aboard Serenity, much of the same relationship continues. She is the more pragmatic Lancer to Mal's sometimes idiotic heroics.
Battlestar Galactica has Saul Tigh, unless he's being an alcoholic or mustered out, then Helo gets the job. He's this to Adama in the original series as well.
Col. Jack Fisk serves the same role on the Pegasus, but his relationship with his commander is quite different. He's scared shitless of Cain, carrying out her orders out of fear—-granted, having your predecessor shot in front of you will do that to a man.
This is never stated openly, but Willow seems to be Buffy's Number Two. Whenever Buffy isn't around, and the Scooby Gang needs a leader, Willow instantly steps up to the plate.
Xander, due to his brief transformation into soldier, becomes Buffy's Number Two for the Graduation Day battle. He was also this to Buffy in the Slayer Organization.
Similarly, in Angel, Wesley takes the Number Two spot in Angel Investigations.
Commander Susan Ivanova of Babylon 5, the station's Executive Officer, is frequently approached by alien diplomats with personal problems. Although her job is to deal with the routine day-to-day matters coming from the station, Sinclair and Sheridan are the military governors of the station and responsible for making decisions and interacting with the ambassadors on a professional level. Later in the series her job gets harder when Sheridan is also running a war (or two). Fortunately, she and Sinclair got on extremely well, and she and Sheridan are Like Brother and Sister and trust each other implicitly.
On Parks and Recreation, Leslie Knope as deputy director is Number Two to Ron Swanson, director of the Parks and Rec department. ...At least officially. In reality, she's the only one getting anything done, since Ron has admitted on camera that he hates government, and plays the Obstructive Bureaucrat to the hilt.
Later, Ben Wyatt is introduced as Number Two to Chris Traeger, and later still, Leslie appears to be grooming April Ludgate as her own Number Two.
Sea Patrol. Lt Kate McGregor, apply nicknamed "XO",is second in command and the leader of the boarding parties.
In Falling Skies Tom Mason is second-in-command to Dan Weaver of the 2nd Massachusetts. This relationship flips as the show develops, although it's quite natural and the two actually become better friends in the process.
In recent Dutch tradition the main helper of Saint Nicholas, Hoofdpiet (Head Pete).
One Paranoia mission introduces the new Mandatory Bonus Duty of Executive Officer, who (in addition to the usual roles) gets a brevet promotion for the purpose of wearing a higher-clearance uniform— the idea is that Commies will mistake him for the Team Leader and concentrate their fire on him instead. As usual for Paranoia, The Computer didn't think this through properly:
Green-clearance Team Leader: All right, men, let's go!
Random bystander: Hey, why are you letting him boss you around?
"Blue"-clearance Executive Officer: Hey, yeah! *shoots the Team Leader* All right, men, let's go!
The command structure for Space Marines in Warhammer 40,000 sometimes has predetermined successors for Chapter Masters, usually if the Chapter Master bites it the Captain of the First Company takes over but in the case of the Ultramarines Sicarius is being groomed as Calgar's successor and he's Captain of the Second Company.
When a member of a squad dies, in most cases, the player whose squad it is gets to pick which model is removed; the rules say this is to represent corporals taking over for sergeants, or extra grunts grabbing the fallen heavy weapon.
During the Great Crusade, the Primarchs (the head of the Space Marine Legions) would usually split the role of Number Two between the First Captain and their own Equerry. The First Captain would be the senior most commander after the Primarch, while the Equerry would be a personal adviser. For those Primarchs who went rogue, the First Captain would become The Dragon while the Equerry would become The Consigliere.
Lester from Galaxy Angel; in later games his role is taken up by Coco, a former Bridge Bunny, and, in her own story thread, the Angel Forte.
In Mass Effect, Commander Shepard starts out as Captain Anderson's Executive Officer on the Normandy SR-1. Once s/he's given command of the Normandy, Navigator Pressley becomes XO.
In Mass Effect 2, Miranda Lawson serves as XO on the Normandy SR-2, as well as acting as Shepard's Handler. Jacob Taylor and Garrus Vakarian can act as unofficial Number Twos, if you're so inclined.
Garrus seems to be the biggest contender here, having the same attitude as a Paragade Shepard, being a leader in his own right, and in canon traveling with Shepard through the entire series. By Mass Effect 3, the Turians are essentially treating Garrus as their Shepard.
In Mass Effect 3, Liara takes over as the unofficial XO of the Normandy, uses her new position as the Shadow Broker to aid in gathering war-assets, while coordinating with the Alliance on the progress of the Crucible project. This is once again shared with Garrus, if he's still alive, who takes up the military part of it, as a fellow soldier and Shepard's longest serving companion.
In the Omega DLC, Bray is Aria T'Loak's official Number Two working to coordinate her forces on Omega, while Shepard is recruited to be her unofficial Number Two, as the One Wo/Man Army working to reclaim the station itself.
Alistair serves here by default in Dragon Age: Origins, due to the rest of the order being wiped out at Ostagar, leaving him as the only other Grey Warden (not imprisoned) in Ferelden, aside from the Warden.
Bann Tegan serves as this for his brother, Arl Eamon, taking over the defense of Redcliffe from the undead attacks, due to Eamon having fallen into a coma after being poisoned.
Knight-Lieutenant/Captain Cullen is this for Knight-Commander Greagoir in Origins and later Knight-Commander Meredith in Dragon Age II.
Amongst the Dalish, the "First" is the apprentice and appointed successor of the Keepers. Lanaya and Merrill are both the First of their respective clans in Origins, while Velanna from Awakening is a former First, having been exiled after she went on a Roaring Rampage of Revenge against the humans she (erroneously) believed kidnapped her sister.
In Dragon Age II, Hawke serves this role to the Viscount during the second act, negotiating with the Qunari on his behalf. This is because the Arishok views Hawke as the most "promising" individual in the city, while the only words he will deign to say to the Viscount is "Begone!".
Aveline and Varric frequently share the role of Number Two and The Lancer for Hawke, throughout the second game.
Varel in Awakening and Bran in II serve as the resident Seneschal for the Warden-Commander and Viscount Dumar.
DAX is the long-suffering second-in-command of the ZEX in Star Control II. He's never actually seen, ZEX says things to him offscreen.
Evil Genius had a character known only as Number 2. She exists only in the tutorial level and provides the voiceover in explanation videos. In her unit description, she is remarked as "The Indispensable Number 2", much in contrast to when Maximillian has her shot at the end of the tutorial.
In Tales of Symphonia, Botta is this to Yuan in the Renegades. Since Yuan is a double agent and has to keep his identity under wraps, this leads to the initial impression that Botta is actually the leader, until the main character gets captured and encounters Yuan, who is then seen giving Botta orders.
In Super Robot Wars Original Generation, Tetsuya is this to the Hagane's Captain Daitetsu, and Sean is this to the Hiryu's Captain Lefina. Sadly, due to Sixth Ranger rules, the only counterpart to the Kurogane's Captain-slash-Ace PilotElzam Ratsel is some nameless mook with his eyes obscured. After Daitetsu's death, Tetsuya takes over as The Captain and Eita becomes his Number Two.
Apparently subverted in Kingdom Hearts. In Organization XIII, every member has a number, with Xemnas, their leader, as Number I. However, it appears that nobody but Vexen actually cares about numbers beyond I. Reinforcing this, Number II, Xigbar, is presented as just another member of the Organization. However, It turns out to be played straight, albeit secretively. Xigbar knows far more about Xemnas's plans and movements than the other members of the Organization, and it just so happens that back when they were both human, Xehanort and Braig had this exact relationship (After Xehanort's other Dragon bought it, that is).
Star Trek: Bridge Commander starts with the Player Character being a new First Officer aboard the USS Dauntless. Then the Captain is killed by a sudden nova, resulting in your field promotion to captain. Commander Saffi Larsen becomes your XO for the rest of the game. In fact, she may relieve you of command if you fail a mission.
The Number Two is Lavitz for Disc 1 until he dies, and then, it changes to Albert. Albert is the Number Two throughout Disc 2 and into Disc 3 until Miranda takes charge during the Mille Seseau arc of the story. When Disc 4 comes around, Rose is solidly the Number Two.
Officially, Barret is in command of AVALANCHE with Tifa as his Number Two and Cloud as some temporary hired muscle. By the time the party leaves Midgar Cloud is the acknowledged leader, with Tifa as his unofficial Number Two. As captain of the Highwind, Cid later takes on the role, taking over the leadership of the party when Cloud is incapacitated and Tifa stays behind to care for him.
Penultimo in the Tropico series is this for El Presidente.
Leeroy is the security lieutenant of the Temple of Phred. He gets reassigned as Tiren's lieutenant after Sal joins the crew.
It has never been established who is General Izor's lieutenant and no rank has been mentioned about any of the Imperial Elite Guard. Sue and Gary seem to rotate as the functioning capacity of this role.
Homestuck: Diamonds Droog was Spade Slick/Jack Noir's second in command. When Slick recruits the Felt, Crowbar becomes the new second in command.
Girl Genius gives us Moloch von Zinzer, who is, to his immense displeasure, Agatha Heterodyne's top minion. As Mechanicsburg is a town filled entirely with minions loyal to the House of Heterodyne, this essentially makes him the second most powerful person in the town.
Tech Infantry has Johanna Ingolfsson and later Xinjao O'Reilly as Number Two to Erich Von Shrakenberg.
In Gargoyles, Brooklyn is promoted to the position of Goliath's second when Hudson decides he's getting too old to be an effective leader and when Goliath's long absence proves such a chain of command might be needed. He proves to be an excellent choice with his calculating personality and talent for tactics.
A more difficult one to spot is Demona's second in command, who is nameless, but is listed as Second. He appears frequently in her past, being one of the first recruited, he questioned her callousness against humans, and even lost his mate when they went against the proto-hunter. He later saves Demona from the Duncan's men, and is one of the few (exactly four) survivors of the rogue Gargoyles. He continues to be allied with Demona even assisting her with her alliance with Macbeth, despite being 139 years old (which is even older than Demona at this point). He dies offscreen in a massacre.
In Beast Wars, Rattrap in the beginning seemed to be Optimus Primal's Number Two, becoming leader while Optimus was stuck inside the alien vessel in Chain of Command. However, by the beginning of the second season, it would seem that Rhinox took over that role, becoming temporary leader while Optimus was dead. On the flip side, Scorponok was Number Two to Megatron until his death, when that role was passed on to Inferno (obviously due to his loyalty and not his intelligence, which seem rather lackluster) Then, during Beast Machines, the role of Number Two for the Maximals went to Cheetor, who took command whenever Optimus was not capable of leading.
Rattrap was still the Number Two as Rhinox was busy looking for Optimus's spark during most of the episode.
In Kids Next Door Numbuh Five was the real Number Two to the leader, Numbuh One. Numbah Two was a pilot and possibly Numbuh Five's Number Two.
Also Numbuh 86, who plays this role to the Supreme Leader, Numbuh 362.
...who herself was once second-in-command to Numbuh 274.
In the second G.I. Joe miniseries The Revenge of Cobra, Flint is Number Two to Duke and takes over command of the Joe team when Duke is captured by Cobra early in the first episode.
Duke and Flint to General Hawk when the latter arrives in the second season opening miniseries, Arise, Serpentor, Arise!.
In the Marvel comics, Hawk commanded the team from the beginning, with Stalker serving as his Number Two. Duke is brought in when Hawk is Kicked Upstairs to a desk job, and Flint is brought in later as a new Number Two. When Hawk is promoted to brigadier general, however, he's also given authority to resume field command, relegating Duke down to Number Two status alongside Flint (although Flint would be featured more, due in part to his ongoing relationship with Lady Jaye, while Duke faded into the background between the Battle of Springfield and the Trucial Abysmia incident).
In How to Train Your Dragon, Astrid falls immediately into this role with her usual talent as Hiccup and his dragon riders fly in to fight the Green Death, particularly when Hiccup separates from the group to to free Toothless, his dragon. This is because Hiccup knows the most about how to communicate and ride with dragons- vital knowledge to the neophyte Riders- and is extremely talented in the areas of invention and innovation. Astrid surpasses him in combat skill and traditional Viking exploits, but because everything about dragon riding is new to the Vikings, she acts as his deputy. (Once Hiccup earns her respect, of course.) She is also responsible for recruiting the first Riders and convincing them to fight the Big Bad.
Teen Titans. Never outright stated in the show, but Cyborg seems to function as leader whenever Robin is AWOL or otherwise unable to lead, e.g the season one finale.
Except during the finale of the fifth season story arc, when the role falls to Beast Boy. True, for most of it this was by default of him being the only core team member still free and active, but when the others show up, he still seems to be calling the shots until Robin's freed from the Brotherhood.
There's also the fact that to most of the team the Brotherhood are new enemies, while Beast Boy had already faced them numerous times when he was a member of the Doom Patrol before joining the Titans.
This is standard practice in most military forces around the world: every officer will either have a junior aide or senior enlisted man to advise them. Occasionally, the job description also entitles replacing the officer in case he takes a dirt nap or is otherwise incapacitated, to maintain operation even during an emergency.
Alan Brooke was the Number Two of Winston Churchill. Theoretically he was the Number Two of King George VI (since the Monarch, by convention, delegates power to the Government of the day) but that was eccentric British Nostalgia rather than a serious governmental arrangement. The Armed Forces are loyal not to Parliament, but to the Crown, and therefore Alan Brooke could not be nominally subordinate to the PM and retain the authority to over-rule any other military advisor the Government might call in. Alan Brooke was also Chief of the Imperial General Staff - the Empire's senior military officer - and therefore in a position to exercise command over Empire and Dominion troops who Churchill had no direct authority over, and this derived specifically from his nominal role as the King-Emperor's military advisor (since Churchill was subordinate to the King in that respect).