FLASH FACT: The war between the Amazons and the Atlantians has arrived. The battle between Diana of Themyscira and Emperor Aquaman will tear this world apart – unless The Flash can fix it!
Flashpoint #5 begins with Thawne taunting Barry for being slow to catch up mentally and physically, and how this world is being torn apart by his friends. Barry asks him what did he do to this world, and Thawne says the beauty of the madness is that this is all Barry's fault, then he shows Barry by painfully resetting his internal vibrations. It flashes back to when Barry learned that Thawne murdered his mother, and he went back in time to stop him by pulling all of the Speed Force into himself. Thawne compares Barry to a bullet through a windshield, and Barry shattered history, and gave everyone he cared about a broken path. Barry, catches up then punches Thawne. Thomas Wayne asks Barry if he was really responsible, and Barry says he was. Thomas says they can still fix this, they just need Thawne out of the equation, then at that moment Thawne beats down Thomas Wayne and reveals that when Flash altered everything, Reverse flash was then turned into a living Paradox, and nothing Barry does can affect Thawne. Thomas then stabs Thawne with a sword killing Thawne.
They regroup with Cyborg, Emily Sung, and the rest of the kids who about to be ambushed until Grifter and the Resistance fire upon the amazons. The enchantress fires at Batman and Flash and hits Batman. Then in the middle of the madness Project Superman joins the fray. Then the planet starts having earthquakes that the planet starts to crack in half. Barry starts to forget his mission, then Thomas tells him to run away before his memories do. He tells him he can save millions and keep his promise which was to save Bruce, then he hands Barry a letter to give to Bruce. Thomas says he can run away from this same as he can leave this world behind because a better one will replace it. Then he says he's sorry for his mother.
Barry runs to his mother's house. He starts to tell her that this is all his fault. He tells her how he managed to save her life, but he can't without the cosmic treadmill. She tells him to focus on himself, but if he does he can't save her. But she asks how many people have died because of this, millions. She says this life won't be erased and she'll be fine with his father. Barry then races after himself to stop himself. When he stops himself he knocked himself out of the timestream, then he starts to see three timelines. Then a hooded woman tells him that the history of heroes was shattered into three, that they were splintered to weaken your world for their impending arrival, and they must all stand together the timelines must become one.
He wakes up in Central City at his desk. Then Barry runs into the batcave, and tells him the story of what had happened. Barry then torments himself on his selfishness, but Bruce tells him it's okay, and if he had Barry's power he'd do the same thing. Barry starts to question why he remembers some of the memories of the other world, he remembers all the memories with his father, he tries to explain it, but Bruce says maybe it's a gift to make it all easier. Barry then tells Bruce, that there's someone who he couldn't save the world without, Thomas Wayne, and he gives him the letter Thomas gave to him for Bruce. Bruce reads it and cries, and he thanks Barry.
This issue not only brings an end to the Flashpoint event but to the "old" DC Universe timeline. The events of this issue directly lead into DC Comic's New 52 relaunch of their entire line of books.