Time to Step Up Commander

The Hero/The Captain has been temporarily or permanently taken out of commission, and The Lancer/Number Two has suddenly found his group declaring him The Leader. But he's genuinely reluctant to take up the role. He may feel guilty for usurping the position, or afraid he's Unfit for Greatness. One or more of his new subordinates in Five-Man Band/The Squad will say "Get ahold of yourself, you're our leader now." a Dare to Be Badass for the chain of command. If the Decoy Protagonist has met his untimely end, this can be the unveiling of the real hero.

Alternately, this can occur when a former subordinate is pressganged or voted into leadership after a Heroic Team Revolt or The Mutiny, whether or not the previous leader is left alive to complain.

See also You Are in Command Now, where the subordinate finds himself in charge more or less by accident, Field Promotion, where a senior character promotes the subordinate as opposed to just one of his peers, and Take Up My Sword, which which it may overlap. If Commander is the character's actual rank, its Commanding Coolness.

Live Action TV

 * Happens all the time in Star Trek.
 * A Specific example would be "Best of Both Worlds", where Riker is faced with this from Guinan.
 * Happens to Colonel Tigh in Battlestar Galactica Reimagined. After Adama is shot, Tigh's wife is telling him that he is in charge now, even though he does not have the character or charisma for being in charge. Then, let's just say things go downhill...

Film

 * In K19: The Widowmaker, the young reactor engineering chief at first chickens out when it is his turn to do some welding in the highly radioactive reactor core. Getting ignored for his cowardice, he mans up, sneaks into the core, and not only does his job, but does ignore orders to come out unless the job is done, and does a Heroic Sacrifice in the process.
 * In Run Silent, Run Deep, Lt. Bledsoe objects to Cmdr. Richardson's obsessive hunt for a seemingly unbeatable and undetectable Japanese submarine. But, when Richardson is injured, Bledsoe carries on with Richardson's hunt.
 * At the beginning of In Harm's Way, Lieutenant (j.g.) McConnell is the command duty officer aboard a destroyer that is docked as the attack on Pearl Harbor begins. With the captain and first officer are ashore at church, he orders the engine room to light all boilers. When there is enough steam to maneuver, he orders that all lines be cast off and that the ship go to open sea. He refuses to slow down for the captain and first officer (who try to catch up to the ship in a launch) to come aboard, as this would make the destroyer an easy target for the Japanese pilots.

Video Games

 * One of your soldiers you can talk to in the pub may tell you that "Its time to step up Gerald" in Kingdom Under Fire: The Crusades.
 * In Final Fantasy VII, after Cloud goes missing and Tifa leaves, Barret talks about taking (back) leadership... but realizes he's not cut out for it (plus everyone present came to the team after Barret's stint as AVALANCHE's leader), so he nominates Cid, who replies "No way. Pain in the ass!" Barret talks him into it, however.
 * Optimus finds himself constantly being praised as leadership material after Zeta Prime bites it in Transformers: War for Cybertron.

Web Comics

 * Order of the Stick: When  Haley is distraught and unable to take action. Durkon reminds her that she's second-in-command, reminds her that , and tells her to take action on the situation. This kicks the rogue into action.
 * Girl Genius: Gilgamesh questions his father's alleged death because they Never Found the Body; Boris agrees, but says he has direct orders to immediately acknowledge Gil's leadership anyway, just to keep the Empire running smoothly.