ANNO: Mutationem: At the Ruthless Rooftops of Noctis City, after getting briefly separated from Ann when the roof of a building collapsed, Ayane worryingly calls out for Ann thinking the worst happened and begs to not be left alone until Ann responds back and affirms that she's alright.
At the end of Batman: Arkham Knight, Batman finally gets the best of the viral Joker in his head, symbolized by him conjuring up a cell in his mind to lock him up in for good. Knowing he's truly, finally beaten, Joker pleads with Batman not to leave him all alone in the depths of his mind:
Joker: No Bats, wait! No! Please! Noooo! Batman: Goodbye, Joker. Joker: No! Bruce! Don't leave me! Please! ...I need you!
In Episode 2 of the Burial at Sea DLC of BioShock Infinite, while Elizabeth is having a mental conversation with her hallucination of Booker as he tries to help her remember why she sent herself to Rapture while she was still omniscient and what the "ace in the hole" is, she turns around to find that he's vanished. She breaks down sobbing and begs him to come back.
Elizabeth: I don't know what to do, Booker, I— (turns around to see he's not there) B-Booker? Booker?! No, please!(falls to her knees and slams the ground with her fists) Please, just don't leave me here! BOOKER!
CookieRun: Kingdom, the Frost Queen and the Lantern in the Snow event has Cotton Cookie beg this of her friend Sherbet Cookie as he fades away into the snow.
Danganronpa 2: Goodbye Despair: At the end of the second trial, the students have deduced the killer is Peko, who killed Mahiru on behalf of Fuyuhiko, as she's been his bodyguard, companion, and assassin since they were kids and was raised to see herself as just his tool. As she prepares to go to her execution, Fuyuhiko finally reveals that he never wanted a tool and just wanted her, before breaking down with this:
Fuyuhiko: Please, Peko, don't go! I need you! Don't leave me!
Miu Iruma in Danganronpa V3: Killing Harmony is suggested to have severe abandonment issues. In her Love Suite Event with Shuichi, she tries to get Shuichi to make a baby with her, believing that it is the only sure way he will not abandon her.
Miu: N-No! I don't want you to abandon me, too! S-So we...we gotta make a baby!
This is inverted in Dead Space 2 when Isaac in a bid to save Ellie, activates the ship that she was investigating so she could get to safety, as Isaac admits that he just wants her to live and where they were would likely end in their deaths. Ellie tearfully responds:
Ellie: ...You bastard....
Deltarune: Tenna, a Darkner based on the Dreemurr family's living room TV, is clearly an ancient model (he's a CRT TV with antennae which are typical of the 1970s, while the rest of Deltarune is clearly set in the 2010s/2020s), and is watched so little by Toriel and Kris that he's not even plugged in anymore at the start of the game. As a result, Tenna feels purposeless and desperately lonely. When Susie and Ralsei voice their desire to stop playing his games, he tries every tactic in the book to get them to keep playing, from guilt tripping, to outright begging, to imprisoning them. After the Fun Gang beats him, Tenna confesses that he just wants people to watch him, that he feels obsolete in the face of new tech like computers and phone apps, and fears being thrown away. If he survives into Chapter 4, you can give him a happy ending by giving him to "Nobody", an anxious shut-in in desperate need of entertainment, who will get enjoyment out of Tenna's programs again.
In the Helios ending of Deus Ex, the last we see of Bob Page is him still plugged into the device he's planning to use to integrate with Helios, unable to escape it and asking Helios (who has already decided to integrate with JC instead) not to leave him.
Trish in Devil May Cry 1 when Dante is leaving her behind after he is angry at her for betraying him over to Mundus.
There is a slightly skewed version in Dragon Age: Inquisition if the player character romances Cullen. There is a conversation shortly before the final battle in which Cullen acknowledges that she has to leave him - to fight the Big Bad. What he can't accept is the idea that she might not return.
Played more straight in the Solas romance, because despite her protests and declarations of love, there is no way for the player character to prevent him from breaking off the romance before the endgame, and leaving as soon as the Big Bad is defeated. It isn't because he doesn't love her - it's because he's really the Dread Wolf Fen'Harel.
Ever17: In Tsugumi's Good Ending, Tsugumi says this to Takeshi as he's pulling off his Heroic Sacrifice. Made even more potent by the fact that Tsugumi's always insisted on being alone up until now.
In Fable II when you are about the leave the "perfect world" your sister Rose begs you not to leave. "Don't go! I don't want to be on my own again." Then she gives out a "Noooooo!"
In Fatal Frame II: Crimson Butterfly, Mayu says this to Mio when she is locked in the repentance cell. She will also say it if Mio runs too far ahead of her.
Henry tells this to Panne in their supports, after he explains his Dark and Troubled Past to her and few later he begs her not to leave him alone.
Henry: Geez, Panne. What WILL convince you to let me stick around? You remind me of the fuzzy animals that raised me, and they all died, and now I... Come on, Panne. Please don't abandon me like my parents did. I'll do anything you want. A-n-y-t-h-i-n-g! Enemies? Gone! Rivals? Kaput!
Also present in some of Noire's talks, especially the event tile one with her neglectful mother Tharja, her Love Confession to a male Avatar and her death quote in The Future Past DLC..
Noire (to Tharja): In the future, you used me as a guinea pig. You subjected me to all kinds of nasty curses on a day-to-day basis! But when it mattered, you used your magic to sacrifice yourself and...save me. But try to leave me again, and I’ll hex you back a hundredfold!
Noire (in her Confession): You fill me with the strength that I never thought I would have. Please stay with me always.
Noire (as her last words in The Future Past): Father, Mother... Come for me... I d-don't want to die...alone.
Velouria's general supports with her mother have her asking for hugs and for the chance to smell her mom's scent. It's related to this trope, since the Future Children of this game were raised in Pocket Dimensions and could only see their war-bound parents once in a while; in Velouria's case, she has missed her "Mama" terribly and is trying to remember her via being physically closer.
"Mom... Don't ever go anywhere... I want to stay with you...forever..."
Niles, despite being a sadistic Troll, does not take abandonment well due to the incident in his past in which his gang left him for dead when a heist went wrong. If he marries an Avatar of either gender, in the original Japanese he'll plead with them to stay by his side and hold his hand while he sleeps.
Ike says this to his father in Fire Emblem: Path of Radiance after witnessing the latter's fatal battle with the Black Knight.
Franzen has a moment where Franz was subjected to an Our Hero Is Dead moment, getting ambushed by the mercury Daemon, succumbing to his injuries and actually dying for a few minutes (a meeting with his father in the Spirit World sends him back to the world of living). His wife, Lefsa, said this trope word-for-word while by his side.
God of War: Chains of Olympus has Calliope using this on Kratos, when he's forced to leave her forever in order to become the Ghost of Sparta again so he can defeat Persephone. The game even twists the knife by making his pushing her away into a button-mashing minigame!
The end of Half-Life 2: Episode Twowhere Eli is killed. Alyx cries over his body and says "Don't leave me..."
At the end of A Hat in Time, just as the Hat Kid is about to leave, she finds all the characters she's met throughout the game hanging onto her spaceship, begging her to stay for more adventures. She pushes them off with a broom and quietly sheds a tear before leaving.
In Heavy Rain, Ethan tearfully uses a variation of this when his attempt at CPR on his son seems to fail.
One of Ashe's possible responses to Tryndamere dying in Legends of Runeterra, tearfully begging him to come back.
Little Busters!: Never quite said word for word, but effectively said a few times by Riki. Most notably, when it's suggested that Rin transfer to another school for a while, he abandons all reason and demands that she stay back because he cannot accept her leaving. In her full route, he accepts her leaving, but only very reluctantly. And when Kyousuke begins to leave forever, Riki demands he stay because he doesn't care about anything else but staying with Kyousuke forever. However, rather than try to convince Riki it's the right thing like he's done at many points until now, here Kyousuke admits he doesn't want to leave just as much as Riki doesn't want him to go, and he's extremely upset and despises that he has to go, but he has no choice. It's eventually revealed that this abandonment complex of Riki's stems from his parents dying when he was young. Since they suddenly left him, he's always been terrified that his friends will as well.
Kaidan uses the trope almost word for word: "Don't leave me behind."
A platonic example in Metal Gear Solid 4: Guns of the Patriots occurs halfway through the game from Raiden to Solid Snake. At this point to his knowledge, Raiden has lost the love of his life (who divorced him and married Colonel Campbell after he went missing), as well as his unborn son (after Rose had seemingly miscarried), had recently underwent a traumatic cybernetic conversion, and is near-death from his duel with Vamp. Severely wounded and at the most hopeless he's ever been, Raiden uses his remaining strength to grab Snake, pleading for the closest thing he last left of "family" to not leave him in his Darkest Hour.
In MiSide, Several of the Mitas you run into in the game want the main character to stay with them, such as Tiny Mita, and Mila after she's spent some time with you. The Yandere Crazy Mita also says this to you at the start of the game, and your rejection of her by wanting to know more about how you got trapped in the game causes her to relentlessly chase after you.
In Ōkami, after you free Kaguya from the prison, she says that she feels that she must go to the bamboo field in Sasa Sanctuary, as though being driven by an unseen force. When she gets there, she meets her adoptive grandfather, Mr. Bamboo. She says that it would have been better if they didn't meet before she left, and you help her unearth a rocket. Mr. Bamboo reveals that he always knew the rocket was there, but it quickly turns into a desperate plea for his precious granddaughter to not leave him alone. When she leaves, the rocket becomes a Twinkle in the Sky, and a Single Tear escapes Mr. Bamboo's eyes... which is a hell of a lot less than what will come out of yours.
In OMORI, Basil has this BAD for Sunny, who is moving out. If nothing is done, then on the final day, coupled with his grandmother's hospitalization and implied death, he kills himself out of despair for Sunny leaving, and should Sunny try and stop him, and he violently attacks Sunny and make him lose an eye and both are taken to the hospital.
Chie says this almost verbatim towards the end of Persona 4 when you've died and are getting encouragement from every character with whom you've maxed out your Social Link.
Persona 5: Shadow Madarame begs Yusuke to come back after the latter told him off to find what he should do after facing the consequences of his actions.
Odd example in Pokémon Black and White in one of the Ferris wheel cutscenes, the girl you're riding with goes over to your side and desperately wants you to hold her until it's over. Afraid of heights, or...
In Professor Layton and the Unwound Future, it turns out that Layton's girlfriend is alive. It was thought that she died in a time machine experiment ten years before, but the machine worked for a split second and sent her to the present day. Unfortunately, her body can't hold and she has to go back to that time, where she'll die in the explosion after all. Professor Layton begins yelling "I don't want to say goodbye again! I can't! I won't!"
Raz: Hey. Hey, you guys! What about me?! Don't just leave me here! You guys?!
Sakura Wars (2019) features a flashback to the time the combat revues of old performed a Heroic Sacrifice to seal away the Archdemon. Sumire Kanzaki, a member of the original Imperial Combat Revue, could not join them since she was no longer able to pilot her Mini-Mecha, leaving her powerless to do anything but reach out to her friends as they sealed themselves away along with the Archdemon and plead with them not to leave her behind.
Similarly, although somewhat more meta, the final confirmation for canceling a World of Warcraft subscription is accompanied by a picture of an orc with a tear rolling down its face, while the form chides you for "making the peons cry".
Silent Hill 2 plays this with an unusual twist involving player interaction: nearing the end of the game, there's a long hallway the player is meant to have James walk through, during which an audio-only flashback plays out James meeting his wife, Mary, on her deathbed, where in her grief-stricken, self-loathing state, she lashes out at him and tells him to get lost. This exchange lasts just long enough for you to reach the end of the hallway and exit through the door, but staying just a little longer additionally shows Mary immediately regretting what she said, tearfully begging James to come back, the implication being that he did not, and that Mary died alone and in utter hopelessness. Ironically, this is a revelation that you can only find if James/you the player stay long enough in the hallway, along with the realization that it's far too late to be there for her.
In one ending of Sunrider 4: The Captain's Return, a drunken Ava admits that she missed Kayto Shields during the six years that they spent apart between this game and the previous one. She asks him never to leave her side again. When he promises her that he won't, she passes out with a contented smile.
This becomes a major plot point in To the Moon as Johnny struggles to come to terms with his wife's death. Most notably seen when Johnny pours his heart out to Isabelle.
Used in Undertale on the pacifist route. The final boss is Flowey's true identity: Asriel Dreemurr. Asriel and the first fallen human died together as children. After being reborn as the sociopathic Flowey, Asriel associates the player character, the latest fallen human, with his best friend. He aims to keep killing and reviving them over and over again so that they can "play" together forever. As you wear him down, he starts crying his eyes out and begs you not to leave him again. Once his soul is soothed, Asriel apologizes and realizes that he was projecting his best friend onto the protagonist, even though they are completely different people. He gives up the souls he stole and accepts becoming Flowey again.
Albedo from Xenosaga. When he first finds out that his brothers aren't immortal like he is, he breaks down crying, begging Rubedo not to die and leave him alone.
In Yo-Jin-Bo, this is the usual course of action in the Bad endings. The pendant pulls Sayori away from her chosen man and leaves them both crying for the other to not leave.