Daitokouji-sensei of Yu-Gi-Oh! GX stuck around as a Spirit Advisor. He actually proved to be more trustworthy after his death, since he was a Double Agent while he was still alive.
One of the best-known examples, Roy Focker in Super Dimension Fortress Macross —Hikaru's "sempai" and leader of the elite Skull Squadron aboard the titular ship.
And in one of the sequels, MacrossFrontier, Focker's death is directly referenced when the current Skull Squadron leader, Ozma Lee, all but telegraphs his death all throughout the episode, going as far as the "pineapple salad" (in this case, pineapple cake) that spelled doomed for his predecessor, as well as similar shots and camera angles. He was rushed to the hospital and survived, and the other characters acknowledge how dramatic it would have been if he had died (almost verging on Breaking the Fourth Wall.) Then this trope hits the other mentorinstead...
This trope is quite frequent in Humongous Mecha Anime. Thus:
Mazinger Z: Dr. Kabuto. He got murdered by his rival'shenchmen shortly after completing the titular robot and handing it over to his grandson.
Kotetsu Jeeg: It happened twice with the same person. Professor Shiba got murdered in the first episode. However he got the foresight to make a backup of his personality in a computer in order to help and guide his son Hiroshiand then it commited a Heroic Sacrifice.
With the danger of spoiling just by mentioning the name of the series: Hikaru no Go. Sai does find peace. The series climax is Hikaru learning to move on.
Rurouni Kenshin has the The Ace mentor Hiko Seijuro, master of the sword school Hiten Mitsurugi, who was first abandoned by his student Kenshin Himura. About over a decade after, Kenshin returns to him to learn the ultimate technique of the sword school they both use, which could only be learned by killing the master. Subverted when Kenshin does learn the technique but did not kill his master thanks to his reverse blade sword.
Naruto. So. Damn.. Much. The idea of people working for the best of the next generation is a major theme, so it suffices to say that teachers have a tendency to die protecting their students or their village. To wit: The Fourth Hokage, The Third Hokage, Asuma, Jiraiya. Even the ones that survive tends to almost die quite a lot.
Subverted with Kakashi for he was revived and Tsunade for she went into a coma and woke up from it.
In The Law of Ueki, when a god candidate helps their student champion in battle, they are automatically sent to Hell.
This happens in The Daughter Of Twenty Faces, although this is more of a Missing Mentor case, as Chiko spends the rest of the series trying to find Twenty Faces.
Trickster Mentor Cross Marian in D. Gray-Man disappeared from the Black Order headquarters while he was under house arrest. Given the amount of blood and the fact that his gun and mask were found on the floor and there were signs of a struggle, he's currently presumed dead, but they Never Found the Body...
Most of Ala Rubra in Mahou Sensei Negima! is in some way incapacitated or made incapable of helping Ala Alba out, but this trope in particular hits Jack Rakanhard. Gets an Obi-Wan Moment trying to take out The Dragon and everything. Of course, like everything else about him, it's awesome.
Ends up averted by the fact he can WILL HIMSELF BACK INTO EXISTENCE, once, twice and apparantly permanently (although he needs an artifical body to walk around the real world).
In Beast King Golion, this was averted with Raible, who was a mentor to the Golion team.
Played straight with Hys, who was a mentor to the princess.
There's also L, who acted as a mentor to Mello and Near. The manga in particular suggests that Near's principal motivation in catching Kira is to avenge L's death - oh yeah, and justice too. That.
Puella Magi Madoka Magica has Mami who gets offed three episodes in. In the most gruesome way possible.
Martian Successor Nadesico has Gai Daigoji...who's entire role was to introduce anime to the crew and die pointlessly.
Koumyou Sanzo from Saiyuki possibly intentionally allows himself to become a victim of this. He sacrificed himself to save Genjyo Sanzo (then Kouryuu) from yokai bandits intent on stealing the sutras... but as Ukoku later points out he should have been more than powerful enough to send those bandits packing without making a heroic sacrifice. This implies he knew exactly what he was doing when he allowed himself to be killed. This is supported by the fact that in his formative years he hung out with a yokai who can see the future and the fact that he'd only appointed Koryuu his successor a few minutes before the attack, suggesting that he had detailed knowledge of what would happen and when.
In Dragon Ball Z we see Future Gohan become mentor to Trunks, it soon becomes a father/son relationship. He is the only one who understands Trunks as a fellow half Saiyan. At the end of the movie, he dies, leading to Trunks having a Heroic BSOD in which he becomes Super Saiyan - the very thing Gohan was trying to teach him.
Earlier on in the series, Master Roshi acts as this; having taken Goku and Krillin (and later, Yamcha) into his home and training them in his own, err, odd, martial art. When Piccolo shows up, Goku is presumed to be dead and Krillin actually IS dead, and Tien Shinhan is the last hope for the future, Roshi uses the suicidal Evil Containment Wave to reseal Piccolo. It doesn't work, and, this being Dragon Ball... he gets better.
Gundam Age has General Woolf, a mentor of the second protagonist, as well as his Expy, Seric Abis in generation 3.
Comic Books
Agent 355 in Y: The Last Man is both recruited into the Culper Ring and trained by the previous Agent 355. One of the techniques she passes on is that the jaw is the most powerful muscle, so when the ex-mentor goes insane and tries to assassinate the President of the United States her successor bites her neck open.
Averted in X-Men by Professor Xavier, who died once but got better (it was never him). And like any mentor, he set a precedent that his students followed time and time again.
However because he's too smart and helpful, most plots especially adaptations will take him out of the story through coma or kidnapping or something until the problem is resolved. He's just not killed by them.
As of Avengers vs. X-Men, Professor X is dead again. We'll see how long that sticks...
Subverted by Emma Frost, who outlives most of her students.
Stick, Daredevil's teacher, who dies protecting him, Elektra and his other pupils (The Chaste) from The Hand. Averted with Master Izo, who outlived all of his pupils. Although, Daredevil: Ninja seems to indicate that Stick got better...
Doctor Strange's mentor, the Ancient One, dies and becomes one with all reality. A subversion, since 1) he deliberately trained Strange as his successor, 2) he asked Strange to kill him, and 3) he's not "gone" in any strong sense.
Fan Fic
Persephone in Divine Blood is killed by her daughter Hecate's ghost while aiding her granddaughter, Eija, in a purification/crossing over. Eija is not amused.
In The Prayer Warriors, after Percy Jackson converts his mentor Chiron to Christianity, Chiron goes off to convert the rest of Camp Half-Blood. Shortly thereafter, one of his students comes back and says that Chiron was killed and eaten by the people there. Death Is Cheap in this fic, but Chiron never comes back.
Obi-Wan's own mentor Qui-Gon Jinn suffered a similar fate.
Obi-Wan was meant to live in the early versions of the Star Wars script, but George Lucas was frustrated in that during the big battle against the death star, he would have had nothing to do. It was Alec Guinness who took Lucas aside and set him straight.
Yoda dies too, although of old age.
Mick, Rocky's mentor, dies apparently from stress about Rocky's poor decision making skills in Rocky III.
Averted with Giles, who makes it through the series alive.
Oh, don't worry, the Season 8 comics took care of that little problem!
Besides, he got shipped off to England for a while. That's as good as being killed off.
Subverted with Splinter in the Teenage Mutant Ninja Turtles movie, although we're led to believe he died at first.
Magi Lune in FernGully seems to exist entirely for this purpose. She appears in a handful of scenes only to later die at the end of the film to pass on her powers to Krysta.
Subverted in Reservoir Dogs: Experienced criminal Mr. White takes a bullet for his young protege, Mr. Orange, survives, then kills said protege after he confesses that he was the rat all along. And only then is he shot dead by the police.
Played straight in Kung Fu Panda with Master Oogway, though at least that's a natural old-age death, and then subverted with Master Shifu at the end.
In Iron Eagle, mentor figure and Retired Badass Chappy Sinclair goes down early on in the assault on the enemy nation that captured The Hero's father, forcing Doug to fight the rest of the battle alone. Subverted in the end when it turns out Chappy bailed out and was rescued.
Averted in The Matrix: Morpheus survives all three movies. In fact, he's the only one of the three main characters to do so.
In The Sting, Hooker's mentor Luther combines this trope with Retirony.
Literature
Jesus Christ from The Bible is possibly the ultimate example of this trope.
In a manner of speaking, John the Baptist also qualifies, as Jesus' "older" cousin and the guy who baptized him. He also qualifies in that he explicitly states he's not here to overshadow The Hero.
Mathin in Robin McKinley's The Blue Sword, one of the elite King's Riders, is assigned to tutor Harry Crewe in the ways of riding and combat. He lives, though, with an awesome scar from Harry's magical healing powers.
The penultimate example would have to be the despised Severus Snape. Before you rush to disagree, recall that he gave excellent advice while foiling Harry's attacks at the end of book 6.
He also gave a very accurate explanation on the process of occlumency, although Harry was not inclined to take it to heart.
Indeed, McGonagall and Arthur and Molly Weasley are Harry's only parental figures that don't fall victim to this trope, and even Arthur comes pretty close in book 5. The author even considered killing Arthur at various points but kept changing her mind.
Dumbledore in particular clearly had to die, because he was the one person explicitly more powerful than Voldemort; the only person in all his life that Voldemort ever feared. If he weren't killed before Harry and Voldemort's final duel, the prophecy that Harry has to be the one to kill him would make no sense.
Depending on your point of view, this is either played straight or subverted with Gandalf in J. R. R. Tolkien's The Lord of the Rings. The wise old wizard, who acts as a mentor to Frodo and later to the whole Fellowship through the first part of the novel, dies in Book II of six. He does come back Back from the Dead again in The Two Towers, but Frodo has already gone his own way by then and can no longer be mentored by Gandalf; while Gandalf himself, with his increased power, becomes a leader rather than a mentor after his return.
Methuselah and Abbot Mortimer are both mentor figures to Matthias in the first Redwall book, and both of them die.
Applies to Beleg in Tolkien's The Children Of Hurin as well, though he's more of a big brother figure. He is unintentionally killed by his fosterling Turin.
That guy, what's-his-name, Obi-Wan Iroh Julio Scoundrel... Brom! That's it! Brom in Eragon.
Fraa Orolo had the misfortune of being revered by the hero and being smarter than the rest of the cast of Anathem combined. So, of course he gets exiled from the not-so-hidden elf village. After a good quarter of the book spent searching for him, they reunite briefly, then he gets promptly roasted by a volcano.
Tad Williams' Memory Sorrowand Thorn plays this deadly straight and justifies it. The Storm King and Utuk'ku deliberately set out to kill the members of the League of the Scroll and anyone else with sufficient knowledge to potentially unravel their Evil Plan before it was complete. Naturally, all of these characters act as Mentors to various protagonists.
Tad Williams' Otherland both uses and subverts the trope. Played straight: Renie's mentor Susan van Bleeck is beaten to death by the Grail Brotherhood's thugs; the old hacker Singh, who helps the heroes break through Otherland's security, is killed by the operating system. Subverted: Mysterious Informant Sellars continually attempts to aid the team after losing contact with them, but manages to stay alive until the climax, after which he surrenders his physical body for a virtual one.
Bluestar from Warrior Cats. Of course, like Dumbledore, she returned after her death to offer more guidance, and has continued to do so for the last three series.
Not to mention Lionheart, Yellowfang, to an extent Spottedleaf, Cinderpelt, and Whitestorm. Mentor figures in the series in general can probably be expected to die (then again, given the series in question...), but it still usually manages to be quite the Tear Jerker every time.
In Codex Alera the spirit of Alera itself is suffering this. She was brought into existence by a mosaic taken from all corners of the country, which was broken. Without it she's dying, although in the last pages she implies that she'll survive in some form. Also, she doesn't actually die until maybe the very end of the book. Even then she might just have grown to weak to appear again.
Honor Harrington's mentor from her academy days, Admiral Courvosier, is killed in The Honor of the Queen.
And another mentor, Captain Bachfisch from her middie cruise, nearly gets killed in War of Honor, but manages to survive with just having his legs blown off.
Averted or Subverted with D'ol Falla, who is The Atoner on top of being the mentor. It's The Messiah who ends up falling into the Bottomless Lake.
Syrio Forel, Arya's "dancing teacher" in A Song of Ice and Fire. In order to buy her time to run away, he stops to fight five guards and a knight with a training sword. He successfully kills or disables the guards, but has no chance against the fully armored knight.
Both played straight and averted in The Hunger Games, with Cinna killed for one piece of rebellious dressmaking too far, but Haymitch managing to survive all three books, and even finding a new family to replace the one he lost, and working on his drinking habit.
Dr. Robert Stadler of Atlas Shrugged proves that a Face Heel Turn does not protect you from this trope, especially when the villains you join are incompetent enough to think that threatening to harm or kill you might pressure your former student into giving into their demands. He promptly decides, "Screw This, I'm Outta Here!" only to be killed by the very weapon he fled to find.
Kosh from Babylon 5, who knew it was coming and was trying to delay it.
Missing Mentor version in Buffy the Vampire Slayer. Wise librarian and all-round Badass Bookworm Giles takes himself out of the series to give his protege Buffy more freedom. He returns eventually and survives to the end, alive and well...though in the season 6 finale it was touch and go for a while.
Giles is the weekly series version of this trope — he can't very well die at the end of an episode so Buffy can fight the bad guy alone, then come back next week. So they did the next best thing: knock him out repeatedly.
They did kill him off at the end of Season 8 (the B.t.V.S. Comic continuation), however. Even then, though, it was more the emphasise that Anyone Can Die.
Subverted in The Cape. Max is shot by Big Bad Chess, gives a tearful dying speech as he lies in Vince's arms... and then realizes it's Only a Flesh Wound.
Max: Dammit, I thought that was it! I wasted that great speech.
Zanki from Kamen Rider Hibiki; generally considered to be one of the better things about the show post-Re Tool.
Narumi Soukichi from Kamen Rider Double - doesn't really count as a spoiler since it occurs in the first episode.
Subverted in Kamen Rider OOO where, after witnessing his mentor Date die in front of him, Shintaro Goto is spurred on to become Kamen Rider Birth for the first time; but then it turns out Date isn't really dead and was just unconscious. He survives. According to Word Of God, Date was originally intended to have been killed in the scene, thus the trope would have been played straight.
Zordon from Power Rangers: Kidnapped almost immediately after quitting the Mentor job, and his first act after rescue was to give one last mentor-y bit of advice and beg for an I Cannot Self-TerminateHeroic Sacrifice. A unique case of the mentor's death actually solving all the heros' problems.
Relic Hunter Sydney's old teacher who first gave her an interest in relics was murdered to obtain one. Twenty years later. Sydney caught up with the killer.
Professor Maximillian Arturo takes the bullet for Quinn close to the end of Season 3 of Sliders. His body is left to be burned along with this Earth, which is being scoured by pulsars.
Notably averted on Stargate SG-1, where The Obi-Wan figure Master Bra'tac is noted for having survived through all 10 seasons of the show, despite multiple attacks by The Plot Reaper and even a feeling of depression in one early episode. He's just that badass.
I am not yet ready to give up. I feel alive Teal'c, like a young man... of eighty. We still have false gods to slay
Manhwa
Interesting version in the Veritasmanhwa. The main character's mentor, Lightning Tiger, is killed right at the beginning of the story (and his pupil receives his skeletal arm in a box as a very creepy Tragic Keepsake). However, LT wasn't old, and he'd only been training the kid for about 2 months. A character attempts to justify it later by saying the he didn't die because he was a mentor; he took on an apprentice because he knew he was going to die.
...Maybe. His heart merged with Terra's after Xehanort struck the final blow, so he might have a chance even if he's not part of the montage of "people Sora has to rescue". As Nomura pointed out, nobody in the series (except Mufasa, and maybe the Riku Replica) has actually died in the literal sense of the word.
The player character's mentor Gorion dies in the first chapter in Baldur's Gate in a battle against the Big Bad. As he's also your foster father, this is also a case of Doomed Home Town.
In Metal Gear Solid, mentor figure Master Miller turns out to have been dead all along, having been killed a few days before the game begins, and impersonated from that point on by the Big Bad.
In Phoenix Wright: Ace Attorney, Mia Fey is killed right after the (very short) first case. She returns as a Spirit Advisor and The Obi-Wan for the rest of the Phoenix games and each game explains her unique state to the player.
Done in record time in Red Faction: Guerrilla - you arrive on Mars and meet up with your brother, who takes you on your first 'mission', recruits you into Red Faction and is shot by the EDF, all in the opening 10 minutes.
Done with the Professor in Cave Story, to the point that if you see him drop several stories and don't try to help him, he stays alive.
In Etrian Odyssey II: Heroes of Lagaard, players meet Flausgul and Kurogane early on and learn several important things about the Labyrinth from them. Once the player learns of their tragic history, alarm bells should be going off... the Player Punch comes upon finding an injured Kurogane and learning of Flausgul's fate. Kurogane hangs on just long enough for the player to take revenge.
Duncan in Dragon Age: Origins dies in the field of battle due to the signal made by the player character and Alistair for reinforcements not being answered by Loghain.
But it's also subverted for Mage Wardens, for whom Wynne fills the role. She's already technically dead, though. The tower also has Wizard Classic First Enchanter Irving, whose fate is entirely up to the player.
Similarly to Duncan, Nihlus Kryik of Mass Effect 1 intended to accompany Shepard on a number of missions, most likely to train him/her as a Spectre, but he is killed at the end of the first mission by the primary antagonist actually Dragon, Saren.
David Anderson is forced to stop being your mentor for political reasons and survives the first two games, only to become the intro-level squadmate in Mass Effect 3. Things aren't looking well for ol' Dave's future, especially when one also considers the high mortality rate of intro-level companions in other Bioware games. In fact, he will die in every ending. However he at least makes it the grand finale, impressive for a mentor.
In The The Legend of Zelda: Ocarina of Time, the Great Deku Tree is cursed from the beginning of the game and dies after he sends Link off on his journey.
Also, Link's uncle dies at the beginning of A Link to the Past, after giving Link his sword.
In Ratchet & Clank: A Crack In Time, Azimuth was created specifically for the purpose of giving Ratchet a mentor figure. And, naturally, he died after going a little crazy and committing a Face Heel Turn, then realizing what he did and pulling a Heroic Sacrifice.
Paladin Magnus in Ground Control, performing a You Shall Not Pass in an Order mission where you have to hold off against an endless wave of enemies. Somehow, self-destructing an Order APC creates a huge crater and destroys the supposed endless waves of enemies.
Prophecies had Prince Rurik, who took on young Ascalonian heroes as members of his personal cadre of warriors and led them on many adventures. He was killed leading his people to safety and was later raised from the dead by the Big Bad.
Factions had Master Togo, head of the Monastery where young Canthan heroes trained and their leader in the war against Shiro. He was killed by Shiro in the penultimate mission.
Bonus points: Several of the Afflicted bosses are actually mutated teachers and quest-givers from your past.
Nightfall had Kormir, leader of the Sunspears and the war against Abaddon. She sacrificed herself absorbing the god's power, and now exists as a god herself.
Eye of the North had Gadd, vitriolic genius and Vekk's mentor/father. Killed while trying to prepare a more powerful golem to assist you in combat.
In Guild Wars 2, no matter what order you've joined, your mentor from that order will die in a Heroic Sacrifice at the Battle of Claw Island.
Giro from Mega Man ZX. Since he gets his hands on Biometal Model Z, it's easily predictable he has to bite it so that you can get to use that model yourself.
Zero in Megaman X. He's watched over X from the beginning of the game, forcing Vile to retreat after X couldn't touch him. Obviously, he's the badass of the story, but he's not the title character, so he performs his Heroic Sacrifice, leaving X to face Sigma alone, with no chance at a last second rescue. Incidentally, the placement of the Vile fight in the remake justifies the over the top dialogue X uses when he faces Sigma, as it happened at the end of the previous stage, and not at the start of the fortress, making X's fury still fresh. And even though Zero gets better, he's been surpassed by X by the time he returns, and they work as a team from X3 to X8.
Web Comics
Happens to Lt.Col. Thomas Knowlton in The Dreamer.
In Homestuck, this has now happened to the Guardians of the Kids. Bro, Mom and Dad were all killed by Jack Noir, Grandpa was Dead to Begin With, and Bec has effectively ceased to exist due to his prototyping.
More like a mentor death contract, considering how sburb/sgrub works. Post-Scratch, the B1!kids switch roles with their guardians. Jade is assassinated by the Condesce and Rose and Dave die in battle against her. John is killed by the impact of the meteor carrying baby Jane.
Done via flashback in ReBoot. To flesh out Bob's backstory we see his cadet days interacting with full guardian Dixon, who gets killed by Killabyte. Since she was shown using Glitch in the flashback, this was easy to see coming.
