The Chains of Commanding are a heavy burden even for the strongest leader, and lately the new guy has been picking up more and more slack so much so that he's practically The Leader of the group. He may not always be right or charismatic, but after going on many adventures with The Team, he's become so influential that he's the leader in all but name.
This can happen slowly or suddenly. Often, the group is thrust into situations they simply can't handle, but the new guy consistently rises to the occasion. The old leader may contribute by over-relying on the new guy or even formally give up his leadership. However, he may cling to his position and insist he's still in charge in this case, the changeover usually happens because the rest of the group has voiced support for the new guy.
- Mobile Suit Gundam Wing Trieze Khushrenada causes one of these. After tricking the Gundam pilots into villifying themselves to the whole world by assassinating the Earth Sphere Alliance pacifist leaders, Trieze's OZ organization is poised to conquer the world... until he chooses to step down as leader in protest over the use of unmanned mobile dolls in future assaults. He is kept in house arrest in an opulent mansion for several months until the Gundam pilots begin to recover and counterattack and the Romefeller Foundation, Treize's aristocratic sponsors, begins to split apart from the inside. At that point, Relena Peacecraft had been installed as Romefeller's leader and, in theory, Queen of the World Nation. Though she was intended to be a figurehead, many of her ideas began to take hold, which raised tensions within the Foundation. Meanwhile, her brother Miliardo had taken control of the White Fang paramilitary group, which controlled most of the military forces in outer space. Since the world was already under a single global command and its leader was unequal to the task of, and unwilling to, prosecute a war, all Trieze had to do was walk in the room and ask Relena to abdicate the title of World Sovereign to him in order to deal with White Fang.
- Parodied mercilessly in Urusei Yatsura when Ataru decides to step down from the class representative role... And finds out nobody remembered he was. Also, he didn't initially specify what role he was stepping down from, so people first believed he was stepping down from being Lum's boyfriend (cue thunderbolt until he manages to explain it's not that), and then from his role as protagonist of the manga (he has to explain he's not stepping down from that role either to every single character save for Lum. Who is convinced that the actual protagonist is herself).
- Inverted in Judd Winick's run on The Outsiders. Jade takes over leadership duty from the frequently bickering Arsenal and Nightwing... except everyone still listens to Nightwing in the field and the team almost universally follows his suggestions instead of Jade's. It's not until Nightwing leaves the team that Jade takes over, and even then it doesn't last long.
- Over in The Avengers, this happened to Hawkeye for a while during the Busiek-Perez era. After leading the West Coast Avengers, Hawkeye found himself frustrated with once again playing second fiddle to Captain America, which eventually led to Hawkeye's decision to join and lead the Thunderbolts.
- In X-Men, Storm challenged Cyclops to personal combat to determine who would lead the team, partly to force him to focus on his wife instead of bearing the responsibility of the X-Men. Storm won and took charge while Cyclops retired to lead a civilian life. However, he's always been in overall command since he rejoined the X-Men several years later. Technically, Storm outranked him for the better part of 20 years, until Xavier made Cyke and Emma Frost the co-headmasters while he was away for some time.
- In Thunderbolts, Moonstone was edging more and more in control when Zemo revealed their secret and so yanked them back to his control.
- In XIII, this trope caused the leader of the revolutionary army to secretly sell out his second-in-command to the dictatorship they were fighting after realizing they trusted XIII more than him.
- Aliens has Ellen Ripley take over as de facto commander of the space marines when their lieutenant has a breakdown during a firefight. Since Ripley is a civilian consultant being dragged along on a military expedition, this requires an interesting balancing act (although the lieutenant himself doesn't protest much).
- The lieutenant is smart enough to realize that the surviving marines will not take his orders and would probably shoot him if he tried to force the issue. They maintain the fiction of him being in command in case they survive and there is a court-martial.
- Star Trek (2009) plays with this. When Pike departs to meet with Nero, he appoints Spock as Captain, and Kirk as Number One. A few scenes later, we see Kirk lounging in the Captain's Chair, lost in thought, as an annoyed Spock walks past...
Spock: Out of the chair.
- Used in Transformers when Megatron is brought Back from the Dead and finds out that Starscream has... well... done what he does best.
Megatron: Even in death, I still rule!
- This happens in Men at Arms. In Captain Vimes' absence by way of One Book Retirement, Carrot had to take over leading the Watch. When Vimes returns, Carrot makes some recommendations to Vimes. Vimes pointedly reminds Carrot that he's still in charge, and then does almost exactly what Carrot recommended anyway. Unusually for this trope, Vimes not only returns to his original position of authority, but gets promoted from a mere captain to Commander of the City Watch, with Carrot as his second in-command.
- In The Amazing Maurice and His Educated Rodents the leader of the rats from before they gained sentience, Hamnpork (they got their names off of labels) feels threatened because of his age and how differently the younger rats think. There's Dark Tan, a big younger rat who increasingly commands the rats, and Dangerous Beans, a practically blind white rat who's their main thinker and mostly ignores their old hierarchy.
- In No More Dead Dogs, a football player essentially becomes the director of the school play in a coup de etat, though the actual teacher directing occasionally tries to remind the students that he's supposed to be in charge.
- Post-apocalyptic Victoria has a peaceful example with protagonist John Rumford and his fellow rebel leader William Kraft. Initially, Rumford is the elected leader of the Christian Marines militia and their support network; but once Kraft emerges as the proven overall leader of a broader coalition, he eventually puts his organization at his full disposal.
- In the Warrior Cats series, WindClan leader Tallstar becomes so old and ill that his second-in-command, Mudclaw, makes most of the decisions for the Clan. With his dying breaths, Tallstar decides that he doesn't want Mudclaw to be the next leader, so he makes Onewhisker his successor instead.
- Happens a couple times in Angel:
- After Angel has a breakdown and deserts his friends, they refuse to take him back when he asks to join them again, until he specifies that he wants to work for them not the other way around. So Wesley gets the job, but he generally defers to Angel in combat situations. Around the time Connor is born, Angel is basically back as the de facto leader (in part because he was not going to listen to anyone or take orders when he needed to protect Connor) while Wesley is technically in charge up until a certain prophecy tears the group apart.
- Gunn's old gang of vampire hunters go through this as Gunn begins to spend more and more time at Angel Investigations. They begin feeling like Gunn isn't part of their crew anymore, and in his place is a new guy who is much more proactive and convinces them to hunt and kill non-violent demons.
- In one episode of Battlestar Galactica, a group is stranded on a planet under the command of a young, incompetent lieutenant. Chief Tyrol, being much more experienced, constantly gives advice. The lieutenant resents this, worrying that he's losing control of the group. Naturally, every time he ignores Tyrol's advice, it goes badly.
- Doctor Who: "Boom Town" plays it for laughs, as Jack briskly starts giving orders about how to surround and overcome their enemy, causing the Doctor to ask who's supposed to be in charge again? Jack apologises, and the Doctor says "Like he said. Nice plan!" Seems like the Doctor doesn't enjoy having a taste of his own medicine, since he invariably takes command away from the actual leaders pretty much as soon as he walks into a room.
- House had a brief Season 2 arc where as part of an official reprimand House was ordered to have another doctor supervise him. Cuddy gave the job to Foreman, but House still pretty much behaved like House, ordering the others around while bullying Foreman into going along with it and doing reams of his neglected paperwork.
- The job of being House's immediate supervisor is traditionally a thankless and terrible ordeal. House will not respect your authority or obey your instructions and you will still be held responsible for the messes he makes (while he escapes longterm consequences like losing his job because he gets results).
- The Walking Dead: Deanna falls in to this in season 6. She's still the official leader of Alexandria and Rick is at least nominally subordinate to her, but he's far more assertive and focused on taking out the various threats to the community. After losing her husband and one of her sons Deanna falls into a depression and starts deferring to him on everything, which causes controversy among the other residents who distrust Rick. Eventually she admits to Rick that he's the leader Alexandria needs, and he's cemented as such when she's killed in "Start to Finish".
- This eventually happens to Luke in Tales of the Abyss as he goes through his Character Development and has more of an impact on the events of the plot. By the end of the game, Tear says he pretty much became their leader.
- AVALANCHE in Final Fantasy VII changes to the point only two of the original members are still there, yet Barret keeps using that name while referring to the Player Party and still calls himself the boss, but does what others say. Later, when Cloud is incapacitated, he voluntarily cedes command to Cid.
- In Super Mario RPG Bowser "recruits" your party to his (at the time, one-man) army and tell you about it every time he can.
- After his FaceHeel Turn, Arthas in Warcraft III occasionally says "No one orders me around" immediately before doing whatever you say.
- Brother claims to be the leader of the Gullwings in Final Fantasy X-2, yet as the game goes on, they start doing what Yuna wants more and more. It bounces back and forth between them.
- Subverted in Mass Effect 3, in that the Alliance still accepts Shepard's command of the Normandy, despite the Commander's reputation being put through the ringer since the last time Shepard was in the Alliance. Even when the Virmire Survivor is promoted to Shepard's old rank (or even higher), s/he still defers to Shepard without question.
- In fact, Shepard's status as a Spectre, and his/her explicit backing from Admiral Hackett and Councilor Udina, results in Commander Shepard discussing strategy and politics on even terms with Admirals, Generals, and other high leaders across the galaxy.
- In Fire Emblem: Radiant Dawn, the leader of the Dawn Brigade is officially Nolan. However, it's Micaiah's Psychic Powers that allow the group to stay one step ahead of the Begnion Occupation Army, and everyone is well aware of this -When she's nearly captured in the opening scene, a Begnion soldier remarks that without her the Dawn Brigade is nothing. When the Dawn Brigade meets up with and joins the Daein Rebellion, Micaiah rather Nolan is named General, however Nolan does not seem to be bitter about this (though he's Demoted to Extra shortly afterward).
- In Dragon Age II, after discovering the corruption of Captain Jeven, Aveline is promoted to Captain of the Kirkwall City Guard, while Jeven gets hailed off to rot in his own dungeons. He later returns in Act 3, attempting to orchestrate a coup to retake his former position, only to be cut down by Hawke and company for his efforts.
- In Fans!, Katherine spends pretty much the first arc complaining about this trope after everyone begins to defer to Rikk's leadership. After she screws up out of desire to reassert her authority and nearly gets everyone killed, it's made official that Rikk's the new leader.
- In The Guild plays with this trope. Vork abdicates leadership and Codex is elected the new leader. Afterwards he constantly back-seat leads, and Codex even starts snarking back at him that if he's going to criticize her leadership, he can have it back! ...and then begging him to, since she was a horrible leader.
- The guild of Gaea Admirers from Noob plays with this. The guild got created as an Instant Fan Club of sorts for Gaea, a player of another faction that the guild members have mistaken for a Double Agent actually faithful to their own faction. Gaea, being a Manipulative Bastard, decides to go along with this and has the guild's members basically be her minons. The trope gets closer to being played straight when Gaea gets tired of her current guild, decides to change factions, is made leader of Gaea Admirers, than leaves it, but the guild's status as an Instant Fan Club holds despite this. We get to see the guy who took over in the novel version of the story and he considers himself to be a substitute leader while expecting Gaea to come back sooner or later.
- Played for Laughs in the G.I. Joe: A Real American Hero episode "Arise, Serpentor, Arise: Part 1" - Sgt. Slaughter puts every single Joe through a refresher course in discipline, as the team has grown soft after a narrow victory against a Cobra assault. He puts EVERY single Joe through his harsh training - even his superior and commander, General Hawk!
- Inverted in Roughnecks: Starship Troopers Chronicles. Rico is promoted to Lieutenant and officially given command of the Roughnecks, with his old instructor Sergeant Zim being assigned as his senior NCO. Rico repeatedly tries to defer to Zim, and Zim refuses to have any of it because Rico is in command and should be making the decisions, even if he lets Zim figure out all the details to make them work.
- Averted in Young Justice; In season 2, Nightwing takes up the reins as leader of the team while Aqualad serves as The Mole in his Father's organization. After completing his mission, Kaldur returns to the team and Dick immediately hands back leadership to him.
- The US system of government is arranged so that, at any given time there might be half a dozen ex-presidents. These usually spend their time doing philanthropic fundraisers, writing or ghostwriting memoirs, or making speeches at political conventions or meeting the leader of North Korea and taking a few pics with him to free hostages. Or whatever.
- Another Political example - H. H. Asquith, the Liberal Prime Minister of Great Britain 1908-1916. From about 1912, he was considered stuffy, outdated and out of touch by many of the people, and of his party - most of whom preferred the dynamic, (comparatively) radical and charismatic David Lloyd George. His clinging to power and relying on traditional peacetime bureaucracy almost cost Britain WWI - things only picked up when a large part of the Liberal party and their Conservative parliamentary allies demanded he step down for Lloyd George.
- Even then, he and his significant minority of followers continued to spar for control of the Liberal party with Lloyd George until he died in 1928 - this is generally considered to have been the reason the Labour Party were able to rise so swiftly and the reason that the Liberal Party had not even an iota of influence over British politics from 1922 until 2010 (and even in 2010, the Liberals were gone - it was their spiritual successors, the Liberal Democrats). Nice going, Asquith....
- Patrice de MacMahon, the first president of the French Third Republic was an ardent monarchist who disliked the idea of republicanism. This led to a constitutional crisis in 1877 when he dismissed the Parliament, only to have the republicans win an overwhelming victory. Since the French constitution provided for a powerful president, there was a great deal of confusion as to who had the power to do what. Leon Gambetta, the parliamentary leader of the incoming republican factions, demanded that MacMahon should submit (to parliamentary power) or resign. Supposedly, MacMahon replied "J'y suis. J'y reste !" (I'm here. I'm staying here.)
- Subverted by Theodora, the Empress Consort of the Byzantine Emperor Justinian. During the Nika revolt in 532 AD, when their life was at stake due to an incident at the Hippodrome, she insisted to his husband, who was ready to abdicate and flee: Isn't purple a lovely colour for a shroud? meaning that she was ready to die as the Empress and she insisted that her husband do the same. The revolt was eventually subdued.