When you hear Superman, who is now locked up in a special prison, says that Metropolis is gone, Lois is gone, their child is gone and Batman turned his back on him and despite everything he did you can't help but to feel sorry for him.
Then he brings up to Bruce that he's also all alone in the world now in terms of people who can understand him since Alfred is dead and all of his Robins are gone with Damian being locked up, Dick and Jason being dead, and Tim being missing (presumably because Superman didn't let him out of the Phantom Zone).
There is a cruel irony in Clark's words to his former friend that Batman is a scared kid still trying to stop two bullets because, as everyone saw in the first game prequel comic, Superman's road to his current position started after he failed to keep two heartbeats coming from one person going.
Life wasn't kind to Alt!Green Arrow. The details are fuzzy, but he started off a billionaire...
Green Arrow: Then everything went wrong. Everyone I loved died. And now my only asset is a small cabin.
Ra's manipulating Harley into helping him by using her young daughter to prevent Harley from killing herself through an Explosive Leash.
Issue #8 revealed that Damian Used to Be a Sweet Kid despite being raised as an assassin, since his first day in action by himself had him not only fighting criminals but helping civilians without expecting any monetary reward from them. He had so much potential before everything went to Hell...
Rewatch Bonus: The $5 Damian reluctantly accepted from the lady is one of Bruce's treasured keepsakes in the beginning of the issue, kept under glass.
Issue #8 also shows just how lost Bruce is without Alfred. He doesn't know what's in the refrigerator, for instance.
Booster Gold warning his old friend Ted Kord that he's tried and failed three times to stop the grim fate approaching him, and assuring him that he'll be there at the end.
"I find one who hurt you. I kill. I good kitty."
In issue #11, Kara's escape from Krypton is just as heartbreaking in the comic as it is in the game. In #12, we finally get to see her dealing with the loss.
Kara: My... my planet. Krypton. I was destroyed. I saw it. I couldn't look away. I watched my world end.
Animal Man's reason for joining Ra's Al Ghul in #18.
How he describes finding a dying animal and being forced to Mercy Kill it.
Animal Man: 10 years ago, I was in Cameroon. I was trying to stop a man intent on killing the last West African Rhino. Not for food. Not for vengeance. Just for sport. I was too late. The butcher had taken his horn. And a poorly aimed bullet was slowly, agonizingly, taking his life. I bonded with him, and borrowed his power. He'd wandered for a year, maybe more, calling with no answer. I sat with it...as it left. It was a giant, but it felt so small. Not because it was dying and afraid. But because it was the last. And it had been so completely alone in the world.
To make matters even worse, the West African Rhino is based off the real-life Western Black Rhino. Can you guess what happened to the last members of this subspecies?
Even in a universe where superheroes exist, entire species of animals are being hunted to extinction by poachers, rainforests are being chopped down, and oceans are being poisoned, in exactly the same way as in the real world.
Alfred is resurrected with the Lazarus Pits... but he's been gone for so long he's brain-dead. And we discover this because Damian is spoon-feeding him and acting so kind to him that his "sister" is pretty surprised to see this part of him.
One could wonder if Alfred could be brought back to life after a long time after his death why no one thought of bringing back Lois.
As of issue 22, Pamela and Harleen seem to be still in love. However, we know that it won't last long. Something bad happened between them...
Issue 23, all animals preserved by Ra's in his sanctuary are killed by El Diablo's explosion provoked by Blue Beetle. They were all the last of their species...
What poaching and pollution deliberately started, Blue Beetle, a young, innocent superhero, accidentally finished.
Issue 34: It seems like Dex-Starr's origin story will be heartbreaking no matter what universe. Whereas his owner was killed by some house robber in the original DC comics, in this universe the family that took him in was brutally murdered by AMAZO on Ra's al Ghul's orders. In one hand, its less brutal than his original back story since in this universe, Plastic Man is willing to take him after his owner's death in but is forced by Batman to leave Dex behind, whereas in the original, the poor kitty was abused by strangers following his abandonment. On the other hand, Dex still tries to defend his family and attack AMAZO, only to be pushed aside effortlessly by the android, and is later shown grieving over his owner's remains. Had Plas managed to took care of him, he likely wouldn't have drawn a Red Ring to him.
Issue 35: When it seemed that Alfred has been fully recovered after being brought back to life, its shown that Came Back Wrong is still in effect. He is bedridden all the time and suffers from memory loss', having forgotten that Dick Grayson died a long time ago and grieves with tears on his face upon being reminded of it.
The turning point in Wonder Woman's backstory as seen in the Annual: Diana finds out Steve Trevor, the man she loves, is in reality a Nazi spy who got close to her as part of a plan to steal the Lasso of Hestia, and killed one of her Amazon sisters while trying to get away. Tearfully she asks him Was It All a Lie?, to which he replies that he did love her, but he loved his homeland moreso. Stoically, she kills him for what he's done and locks that part of herself away. Even knowing what she is, it's sad to see her in such pain (and certainly explains why she is what she is).
It's revealed that Jonathan and Martha Kent have taken up residence in the Fortress of Solitude because they were exiled from Smallville and had their farm burned down simply because they found and raised an innocent baby that turned into an alien tyrant, which they couldn't have predicted.
Pa Kent calls out Batman for not being there for Clark to comfort him after his tragedy, and Batman agrees. He is genuinely regretful that he didn't handle things better.
Batman: I'm sorry, Mr. Kent. I tried to do what I felt was best. But I failed him. Pa Kent:(looking away) We all did.
No one tried to go comfort Superman as he was grieving alone in the fortress after the tragedy that fell on him: not Batman, not the Kents, not the Justice League. The only one who went to the fortress was Superboy, and all he did was give him harsh words for killing the Joker. All he could hear before and after that were the voices of people suffering and dying all over the world. On top of that, the last word his wife told him was to go and save the world. So not a single one of them is free from blame for what and how bad things turned out. It seems everyone who heard Pa Kent knew they really failed Clark, as all of them looked guilty when he said it.
Martha then tries to comfort Bruce:
Martha: You kept Clark alive, didn't you? That's why he's in prison and not executed. You haven't given up on him. (Martha puts a reassuring hand on Bruce's.) Batman: ... I'm honestly not sure.
After six years of being trapped in the Phantom Zone most of the Titans are finally free only for Zodd to sneak behind them and kill Robin (Tim).
Issue 38 reveals that Batman retrieved a sample from the fear gas mixed with Kryptonite the Joker used on Superman, but admits that he could never bring himself to use it on Clark, not after what it made him do.
Issue 55: Hal Jordan becomes a Red Lantern. What was it that gave him enough rage in his heart to become one? What or who did he hate enough to obtain so much rage? Himself.
Issue 56 when Ms. Kent talk to Superboy, who was worried since he had the heart of Zod inside him,about if evil could be transferred via organs then she breaks down crying and say that Clark heart was never evil it just could not take what happened.
Issue 64: Sinestro's death. Even after all the things hes done, he dies proving that even he can be redeemed. In his final moments, he decides to reveal the truth about what happened to his wife to his daughter, telling her that hes responsible for her suicide, and apologizes for not being a better man. The real clincher? His ring transfers to his daughter.
In the second annual when Ms.Kent visit Clark and they hug it's visible how much she is hurt to see where her only son has ended up.
The flashback shows a better time between Clark and Bruce. Even those who have read the first game prequel comic will wonder how did it reach this point.
Batman visiting Clark and finally telling him that he is sorry about what happened to lois, as well as admitting that he should have been a better friend to Clark after her death.
As Batman is leaving, Clark is sitting and crying at the mention of his wife.
The cover itself shows a comparison between the past and present. It's really heartbreaking.
The dialogue between Supergirl and Superman, while often having a Deadpan Snarker or Broken Pedestal vibe, sometimes emphasizes the "broken" part and how tragic the situation is, Supergirl really not wanting to fight her cousin.
This dialogue between Batman and Robin (Damian Wayne, who killed Dick Grayson by accident and hasn't been forgiven) is just COLD BLOODED:
Batman: I don't have time for this, Damian. Robin: A good father would make time. Batman: A better son would deserve it.
Robin: I didn't murder Dick, Bruce! Batman: No, your temper did, Damien! Robin: It was an accident!
On a similar note, a clash quote between Batman and Wonder Woman implies that Batman has completely given up on his son. When Diana tells him that "Damian despises you.", Batman nonchalantly replies "You can have him."
The scene in the story trailer of Superman holding a dead Lois along with a sonogram of their dead child and hearing the sound of its last heartbeat, before releasing a Death Wail when he realises they're gone forever. It's a sad reminder of the fact that as cruel as he has come in enforcing order Superman is still a man grieving his family.
This leads to an expression of solidarity from Atrocitus in-game.
Superman's originstory is already bad enough. Supergirl's turns it Up to Eleven. Kal at least was an infant when Krypton was destroyed; Kara was a young woman when she saw Brainiac kill her people and destroy her planet. Her parents sacrificed themselves to save her, and the only other survivor (as far as she knows) is her baby cousin. Then, after spending decades apparently in stasis, she finally reaches Earth to find that her baby cousin became a hero, turned bad and set up a dictatorship, and was overthrown and locked away by a planet that fears him more than anything else (and when he breaks out and tries to take over again, he makes it clear that she can either help him or be dealt with like he has done with many other threats to the Regime). Oh, and the monster who destroyed Krypton has come for her new home too.
Upon arriving on Earth, Supergirl was lied to by Diana and Black Adam about who Superman was, what he had done, and why he was imprisoned. She makes it clear, once she finds out what the Regime stood for, that she would have no part in it and fight against it with all her Kryptonian might. Seeing her baby cousin has truly become a monster is heartbreaking, but even worse when you consider that Kara's mother told her to protect baby Kal-El, to teach him the ways and history of Krypton and the House of El. Kara clearly takes upon herself some of the blame for who Injustice!Superman became, feeling that she failed him by not being there for him.
What makes it a bit saddening is that despite his desperate efforts to go back to his timeline, Reverse-Flash is clearly torn up by the fact that he can never go back home.
The final conversation before they fight for the last time between Batman and Superman.
Superman:Fighting on the same side, it felt like old times. But I guess we both knew it would end this way. Batman: Do you remember that night? When you told me Lois was pregnant? Superman: You knew. Even before I said anything. Batman: That was a good memory. Superman: From another lifetime. Batman:...I miss the people we were then. Superman:...Me too.
What makes it even worse is that after coming within an inch of redemption, Superman decides to immediately follow this conversation by sucker punching Batman. It just drives home how far gone the Injustice version of Clark is.
After the the other heroes leave the meeting table, Batman and Superman are left at opposite ends of the table. We get this exchange:
Just goes to show that all these people (except for Supergirl) used to be friends and comrades. Even after doing an Enemy Mine against Brainiac, it's still clear that both Bats and Supes still don't get along.
And just when you thought that Batman and Superman (and by extension, both sides of the Justice League) have patched up their differences despite their mutual animosity, you're proven spectacularly wrong as immediately after Brainiac's defeat, both of them start to squabble over what to do with him, with the Man of Steel arguing that psychopathic monsters like Brainiac, the Joker, and Gorilla Grodd deserve to die, while the Dark Knight states that even if they kill the Coluan, he thinks they're not sure if they even can reverse what's been done without Brainiac and that acting too hastily could cause them to lose more cities. Even though both Superman and Batman want to heal and patch up old wounds, their competing ideologies make it clear it's not going to happen overnight and will them take a long time to fix.
They're not given that time. They immediately come to blows, battle lines are drawn, and the final stage of the game is a Justice League Civil War.
The various scenes clearly show how the Joker has left a legacy of cynicism and bitterness post-Metropolis. Posthumously, not only did he create a wedge between friends who were once inseparable Heterosexual Life-Partners and paragons of justice into bitter Arch Enemies, his actions also caused the once-mighty Justice Leagueto split into two opposing camps, all due to a clash of ideas on traditional heroics and solving crime. To make matters worse, Doctor Fate notes that the havoc Joker unleashed has caused the Lords of Order to decree that humanity is only capable of only chaos and back Brainiac's schemes, and have warned that if Batman and Superman keep on fighting, then they themselves will support an even worse threat than Brainiac.
After Harley is run through with a sword by Wonder Woman,, Kara goes to speak to Superman about what happened. At first, she thinks that Superman is every bit as upset about Wonder Woman's actions as Kara herself. But when Superman makes it clear that he completely approves of Harley being executed, if not the timing, the heartbreak in Kara's face is plain as day. And made even worse by her next few words:
Kara: Everywhere I go, people are afraid of this! (touches the S-Shield on Superman's chest) Now I know why.
Watch Kara's reaction when Superman angrily declares that humans have slaughtered each other for millennia and that he finally stopped that violence. She's gotten over her initial shock and the devastated horror etched into face is heartbreaking. If you look carefully you can ever see her shaking her head slightly as if not believing this is happening.
The fact that Superman could not save all of the captured cities including Coast City. Hal, ever the Determinator, urges Superman to keep trying, but Superman can only apologize.
When Superman is apparently killed by Brainiac's ship, Supergirl is seen sitting quietly at the edge of the crater left behind. When Batman and his allies arrive, she believes that Batman thinks this is the best thing to happen during Brainiac's destruction of Earth. Batman tells her that she couldn't possibly be further from the truth.
In one intro, the Flash pleads for Captain Cold to stop, pointing out that all the murders won't bring his deceased sister back. Cold nods and replies with a quiet and heartbreaking "I know, Barry" as opposed to the Berserk Button her death usually is for him, showing how he's still just a deeply grieving big brother underneath the grumpy, bitter exterior.
Though Batman's ending finishes the game on a cautiously optimistic tone, Kara is utterly heartbroken. She's witnessed her family's symbol, meant to inspire hope, be warped into a symbol of fear and terror associated with a brutal totalitarian regime. Worse, all of it happened and she was completely powerless to stop it, locked in stasis while Superman tarnished the House of El, possibly irreparably. And even worse, the reason Superman did everything he did could have been avoided if she had been there to help him. She feels she failed both her cousin and her family.
Grid. Amidst his general dismissal of the cast, there are a few intros that showcase his desire to achieve emotion:
Grid: Your wife's disease is tragic. Mr. Freeze: What do you know of my pain? Grid: That I would give anything to feel it.
Right before Kara and Damian fight the later says that Superman was more of a father than Batman could ever be. Damien said this in the first game right in the face of his father and now we ask and wonder again if a tyrant Superman is more of a father than a good Batman then what kind of a father he would have been if he didn't lose his wife and unborn child and remained one of the good guys.
In Batman's ending, when he apologies to Kara, she asks for what and he replies with this:
Batman: I couldn't save him.
Let's just say 80% of Mr. Freeze's intro dialogue and leave it at that.
Remember Doctor Fate saved Black Canary when she was almost killed by Superman? He went against fate in order to save her. Now one could wonder if he could see other people's fate and even change it why didn't he help Superman save Lois ten years before all of this happened. He was asked this by Cyborg. The answer will shock you. He just let fate follow it's course. This equal saying that Lois, her baby and the four millions of people in Metropolis didnt matter and thus weren't worth saving.
In a fight against Reverse-Flash, Bizarro will tell him that he wants to "crush you, save Lois!" Reverse-Flash will harshly reply, "Oh, it's way too late for that." It's sad that somewhere in Bizarro's cloned brain, he has memories of Lois.
If a clone has memories of Lois then what of the original, who was deceived into killing her, heard her and their unborn child's last heartbeats and held her body in the destroyed Metropolis?
No matter how many times Damian says that Nightwing's death was an accident no one is willing to listen to, nor believe him, his father least of all. From his voice alone, one can tell how much this hurts him. It's especially bad because it really was an accident.
Starfire's ending has her reminiscing on happier times with the Titans but now feels incredibly lonely without them. Raven is now serving Trigon (which would explain her sudden disappearance after the first game), Cyborg is working for Superman in the Regime, Beast Boy has gone missing and presumed dead, and of course Dick died. Turns into a heartwarming moment when she finds new friends in Blue Beetle, Supergirl and Jason Rusch.
Because of the lineup of the original Titans resembling the animated series in 2003, this ending plays out like one of the episodes in the show, "How Long is Forever", where Starfire is flung into the future and the Titans have split up, only it's sadder here because all of the members, save for Starfire, are either irredeemable, dead, or missing... and this isn't because of her being missing and her team split apart, these whole events transpire when Starfire was in the present timeline (albeit getting sent into the Phantom Zone), 'finding a portal to undo the past' will never be an option.
A match between Starfire and Cyborg will have her asking Cyborg if they want to share some pizza after she wins. After seeing the ending of her Arcade story, it gives some tragic subtext to their banter. This also gives a tragic spin for Cyborg's otherwise heartwarming ending: He might have found himself a way to redeem himself, but Starfire would probably never accept him again.
Another starts off with Cyborg suggesting a friendly match, only for Starfire to call him out for joining the Regime. Given his response, he may be too far gone in the Regime to the point where their relationship may already be beyond repair.
If Starfire faces Red Hood, they will sometimes mention Dick Grayson and how much Koriand'r misses him. From the way Jason's speech tone changes when Dick is mentioned, you can tell even Jason is affected by his adopted brother's death.
Even for those who enjoyed the newer Titans incarnation, it will sting some of its fans. In there, Starfire was being the Cool Big Sis of Damian Wayne as he developed into a true Titan. In here... no way that's going to happen since Damian's accidental murder of Dick, combined with him betraying his father for Superman, would give Starfire real reasons to hate him.
Driven home in one of her mid-match victory lines against Damian:
Starfire: You took him from me!
Starfire calls Dick "My Star-Crossed Soulmate" in her ladder ending. That should drive home the depths of her pain for even the most casual DC fan.
It doesn't stop there. The prequel comics reveal that Ivy once actually reciprocated Harley's feelings for her. This means that Harley used to have a partner who loved her as much as she loved them, and now she's gone.
This exchange between Starfire and Black Manta:
Starfire: You hide a wounded heart. Black Manta: I buried my heart with my father. Starfire: Vengeance cannot bring him back.
The Flash's intro dialogue against Scarecrow shows that even a Badass Boast can become this:
The Flash: I've got nothing left to fear!
Scarecrow: What makes you say that?
The Flash: Because I've lost everything else.
Raiden expresses quite a bit of sorrow over the fate of Liu Kang in a few intros, showing he still hasn't got over losing his beloved pupil.
Reverse Flash: There's blood on your conscience.
Raiden: The death of Liu Kang haunts me still.
Reverse Flash: That's why you don't have a future.
He also is suprisingly perceptive on Batman's internal pain and takes the moment to call out Damian for his ungrateful attitude.
Raiden: You bring Batman nothing but sorrow.
Robin: You say that like it's a bad thing.
Raiden: It burdens his already troubled soul.
Raiden's ending, where despite his best efforts, Kent Nelson dies of his wounds in Black Canary's arms. Fortunately, he manages to turn this around by forming Justice League Dark to protect the planet from the Lords of Order in his memory.
Firestorm's Arcade ending: he/they kill Brainiac by destroying his ship, which also destroys all of the cities aboard it. Overwhelmed by grief at this tragedy, the two halves of Firestorm give up on being a superhero.
Atrocitus' Arcade ending is similar: in killing Brainiac, he destroys all of Brainiac's collection, murdering billions of innocent souls. Though an accident, this is a crime so horrible that his own Red Ringbearers turn on him in fury. Thankfully, it then veers into Heartwarming.
June Moone's prescence in this game, she's visibly scared in gameplay and in most intros. She either desperately asks other combatants for help or to kill her. In intros with Brainiac, Scarecrow, and Joker, she's on the verge of tears as she begs for Enchantress to take over, as she is utterly terrified of fighting them; while with Dr. Fate, she's actually hopeful. The way Enchantress cruelly mistreats her is also a little tear jerking.
Dr. Fate: Two voices in one mind. Enchantress:(smug) I'll silence June's conscious soon enough.
Enchantress' ending, as Nightmare Fuel inducing as it is, is pretty tear jerking. Brainiac mistakingly attempts to absorb Enchantress' power, and both are presumed dead. June is seemingly free and describes her new normal and happy life, including getting her job back and having a date, but her happiness is cut short when Enchantress takes over her again, and makes plans to conquer the multiverses. June screaming as she loses control again makes the entire ending even sadder for her.
In several of Starfire's intro quotes with the Teenage Mutant Ninja Turtles, she admits that (Dick) Grayson would have enjoyed their company and respected their talents wistfully.
For any Flash fans, the exchanges between Flash and Captain Cold, since there was at least a Villain Respect for each other at worst, and now it's all gone because of The Regime, one that Flash realized was monstrous.
Captain Cold: I'm going to kill you Flash. Flash: We've always been civil, Snart. Captain Cold: The Regime changed that.
Flash: You have to move on, Snart. Captain Cold: Too late. My heart's frozen. Flash:(pleading) Let it go.
Flash: Murdering people won't bring Lisa back! Captain Cold:(softly) I know, Barry. Flash: I can't let you give up on yourself!
Then there's Leonard noting Kara looks exactly like Lisa — but the "S" on her chest makes him unable to call her a friend.