- The scene where Barry meets his now alive mother. It's heartbreaking thinking about meeting someone you loved and was dead for a long time.
- The Flash' memories being replaced by new ones. Thinking that some of your proudest moments are being replaced doesn't feel right.
- Barry goes to try and visit Iris in the Flashpoint universe at her place of work. She turns, seems to notice him and smiles... only for it to be shown she was actually smiling at another man carrying a small girl right behind Barry; her husband and daughter. It's definitely not the saddest thing in the story, but having Barry seeing his wife Happily Married to another man with a child in another life must have been difficult for him.
- The entire third act. That whole war is pretty much just one major Tear Jerker.
- The very end, when Diana, upon the imminent destruction of the British Isles via nuclear explosion, cradles Arthur's corpse as she waits for her own death.
- Superman, the very embodiment of a mighty hero, being little more than a weak, emaciated shell of a person who we first see cowering in a corner like an abused dog in the Flashpoint universe.Kal-El: (clinging to Flash) Friends...?
- Barry assumes that Professor Zoom changed something in the past to create the FP!Universe. He eventually finds him but after a short fight he gets beaten down by Zoom and Zoom reveals he didn't do anything to create this world, Barry did. Barry went back in time to save his mother from Zoom, and in the process created a Time Boom that changed certain events in history just slightly, but enough to cause the apocalypse. Zoom is sure to rub in how this is all Barry's fault.Flash: I just wanted to save her.Zoom: Her hero. How noble. Oh wait, you didn't stop JFK from getting assassinated, or make sure Hitler stayed in art school, you saved your mommy. You missed her, and in a supreme act of selfishness shattered history like a rank amateur. Turned the world into a living hell moments away from destruction. And I'm the villain?
- Barry having to stop himself from saving his own mother to save the world. Sometimes, you just have to accept what you can't change.Mom... I'm so sorry.
- The way his voice wavers and breaks... It's clear that this was the hardest thing he's ever had to do. And despite his ability to travel through time, he can never do it to save his mother, because he knows what would become of Earth if he did.
- Seeing Batman of all people shed tears over the letter his father made Barry deliver to him.
- The fact that Martha Wayne became the FP!Universe's Joker. It adds a whole new layer of tragedy and poignancy to her and Thomas' relationship, both as grieving parents and enemies.
FP!Batman: You'd be amazed the monsters this world can create.
- And the way Thomas describes what she became, even in the midst of everything else that's happening.
- FP!Batman in general. There's a reason why it's said that a parent should never have to bury their child. Just as Normal!Batman never stops thinking about his parents, clearly not a day goes by where FP!Batman doesn't desperately miss his son, even if he hides it with cynicism and drinking.
- Which makes the similarities between Normal!Batman and FP!Batman aka son and father all the more heartbreaking. Whoever it was who donned the cowl, both of them do not fear death, and they cannot stop missing the family who was taken from them too soon. It hammers in the tragedy of a young family separated by death, no matter which side of the thread it's viewed from.
Tear Jerker / Justice League: The Flashpoint Paradox