Flash first appears while being contacted by Batman, quickly racing from his home and suiting up before arriving in Metropolis in a near instant. Batman tells him to search every area Superman couldn't from the sky with his enhanced vision. Flash does so and when he returns to Batman, informing him that he has found something. He quickly races himself and Batman to S.T.A.R. Labs where Flash had discovered the body of one of Batman's foes, the Scarecrow, murdered with a smile on his face.
When Wonder Woman reveals The Joker has hijacked a submarine and Superman has carried it onto land and flown off battling Doomsday, Flash carries Batman and races the duo to the sub where the rest of the Justice League has gathered with a captured Joker and Harley Quinn. Batman investigates the sub after warning Barry not to follow him in when he sees the Scarecrow's fear toxin. Batman interrogates the Joker and suddenly tells Flash to investigate the sub for the nuclear missile, but when the Joker tells him not to bother, Batman understands what is truly going on and Flash along with the rest of the League witness Metropolis' destruction.
The Flash helps Hal Jordan rescue and gather the outlying areas outside of the fallout zone. The two discuss Superman's whereabouts with Barry saying he thinks Superman is still in the city and his communicator is off. He surmises no one else can enter the destroyed city because of the radiation.
Barry is next seen among the gathered heroes called by Wonder Woman to the Justice League's Watchtower, where they are informed of the kidnapping of Superman's parents, by one of the Flash's own Rouges, Mirror Master. While Hawkgirl, Shazam and Cyborg deal with three of his other enemies, Flash battles and interrogates Captain Cold and learns of the villains dive bar, World's End. Flash and Wonder Woman later crash the bar and attempt to capture Mirror Master, but he attempts to escape into his mirror dimension only to be ousted by Raven. After Wonder Woman interrogates Mirror Master with her Lasso of Truth, Flash delivers his technology to Superman in Bolivia and the Man of Steel uses it to rescue his parents.
The Flash travels alongside Superman and Wonder Woman to Australia where they are breaking up a civilian protest in response to their arrival. A young man suddenly steps forward and reveals himself as a new hero who challenges Superman and Wonder Woman, demanding they leave. The Flash watches the battle, noting the hero looked strong, but quickly realizes he wasn't strong enough to battle Superman and Wonder Woman.
The Flash watches in stunned horror as Superman and Wonder Woman subdue the hero, shattering his spine in the process. Though he knew he had a chance to act, the Flash only stood there. As Wonder Woman forces the protesters to leave, the Flash suddenly races off to get the fallen hero an ambulance.
As he races away, he is suddenly contacted by Batman. Though surprised to hear from the exiled hero, he follows his directions and arrives at a laboratory in Canberra and meets Doctor Norris, who reveals the hero's - Galaxor's origin. To Barry's shock and further horror, he learns Galaxor was a fan of the Justice League and that Barry himself had once signed a picture the two had taken together.
Overcome with confusion, Barry flees to the Nullarbor, and heads straight for the world's longest road. Through an internal monologue, he reveals he comes here often to think, but is now only here to run. Before he begins running though, he sees the body of a dead kangaroo, and notes it was probably killed by the passing truck. He suddenly sees Galaxor's broken form in the animal's place and is overcome with remorse. Questioning his and the League's sudden course of action, Barry flees in a sudden burst of speed, refusing to think of the incident anymore.
Later, when Superman and Wonder Woman arrive at Arkham Asylum to remove the more dangerous inmates, though not seen, Batman realizes it is the Flash who caused Zsasz and Mad Hatter's disappearance using his super-speed.
When Harley Quinn releases the inmates to attack the heroes, the Flash follows after Superman, Wonder Woman and Nightwing when Solomon Grundy rises from the floor and grabs Robin. The Flash goes to help Wonder Woman after she is backhanded through several walls by the super strong zombie. He is then seen alongside Superman, Wonder Woman and Batman when they return to the upper level of the Asylum and bows his head in depression when he sees Nightwing has been accidentally murdered by Robin.
Though not seen, the Flash is the one evacuating civilians from a city Black Adam is attacking.
The Flash is with the rest of the Justice League when Lex Luthor requests to join them in their crusade to bring peace to the world and is shocked when Luthor reveals he knew his identity along with the rest of the League's.
Flash informs Wonder Woman of Hawkgirl's kidnapping at the hands of Captain Atom, Huntress and Black Lightning. Barry becomes upset when Luthor suggests they recruit more into the League and declares they need to find Hawkgirl, when she herself supposedly appears before the League.
Flash argues with Superman and Wonder Woman over their current course of actions after Hawkgirl suggests they start working with the world instead of for it. The Flash reminds both of them of their battle with Aquaman's Atlantean fleet as well as moving Atlantis itself into the desert. He also brings up Galaxor, reminding Superman that the young hero was crippled and in a coma after his encounter with the League. Robin manages to point out Batman's tactic of trying to divide the League up and Lex calms everyone down by suggesting they communicate with the people they're trying to help.
During the Parademons' invasion, Flash is the first to rush to the teleporter in the Watchtower and demands to be sent down to Earth to stem the loss of life in Paris before Cyborg informs him and the rest of the League of the Parademons attacks across major cities all over the world.
Flash is then seen rescuing a woman in Mumbai from a group of Parademons. Barry attempts to save a second civilian when Superman suddenly appears in front of him, speaking to him at superspeed. Flash wants this to wait but Superman explains he can't talk to anyone else as in the time it would take to talk to them, thousands more would die. Clark explains to Barry what Kalibak told him and though Barry thinks they shouldn't give stock to the villain's words, but Superman agrees that things need to change. Flash asks, "What are you suggesting?" When Superman exclaims that he wants to stop treating the villains with kids gloves, Flash is shocked when he realizes he is suggesting they kill the Parademons.
Superman explains he doesn't want to murder the monsters but can't live with the fact every second they try to subdue them, more people will die. Flash only tells Superman, "I think you've already made up your mind. You didn't come to me to talk. You came to me for permission to kill. I'm sorry Superman. I can't give it to you."
Superman brokenly asks Flash if he can think of any other way to save as many lives as possible...and as Clark flies away, Barry whispers "No."
When Superman unleashes the full extant of his power to destroy all the Parademons, Barry numbly looks up into the sky as it rains ashes of the vaporized monsters while the people cheer around him.
An angry Flash confronts Superman in the Watchtower, shocked that Superman is letting Lex Luthor use Kryptionian technology to create an army of super soldiers. Superman agrees that it seems extreme, though Barry calls it mad scientist territory. Superman suddenly asks Flash if he knows how to play chess.
Caught off guard, Flash explains he played a little as a child, and after Superman asks him how quickly he can learn, the Flash accesses a Watchtower computer and learns chess at superspeed in less than a second.
As Superman and Flash sit down with a chessboard between them, Clark asks Barry how fast he can think, and after a moment of hesitation, Flash admits he can think, "Fast. Very fast." As Clark and Barry play at superspeed, Superman tells him he wants to get rid of all the guns in the world before checkmating Flash.
As they play a second game, Superman says that together he and Flash could get rid of most of them before getting the second checkmate. Flash agrees but says that they have to let the people give them up willingly or else they would be resented. Superman counters that they would be alive to resent them, and when Barry points out they would rise against them, Superman says they would come at them with sticks.
When Flash asks what they would do next after taking all their guns, Superman asks him how many lives he has witnessed be ruined by guns. Flash then tells him cigarettes far more people than guns and when Superman asks "And?" Flash says they take their cigarettes after taking their guns before getting his first checkmate.
He then says they imprison anyone who speeds in a car, leaves a dangerous dog unchained and ultimately kill anyone who doesn't recycle, pointing out if they're going to go in this direction, that is what they ultimately must do. All the while, Barry continues to make checkmates against Superman.
Flash is present along with the rest of the League as Luthor presents and explains the functions of the enhancement pill.
Flash is present as Wonder Woman reveals to a small gathering of fellow League members that Batman has been spying on them using Martian Manhunter shape-shifted into Hawkgirl's form. Flash is in disbelief over such a revelation, calling it crazy even by Batman's standards, though he is silent as Damian tells them none of them truly know his father.
Flash says nothing else as Superman prepares to broadcast Batman's plans and secret identity to the world, though becomes shocked when the Watchtower's systems are all knocked off-line, including life-support, with the League realizing Batman is behind it. Barry is horrified Bruce would endanger his own son to protect his identity, though they are all saved thanks to Superman and Wonder Woman working together to safely land the Watchtower on Earth.
Flash accompanies Superman, Wonder Woman and Green Lantern to the Batcave to negotiate Hawkgirl's release. Though Superman insists it will be a conversation only, when Hal points out all the 'big guns' they're bringing for a conversation, Barry reminds him, "It's still a conversation with Batman."
When they arrive, Flash is confused as to how they approach this but when Batman steps out of the cave, he listens as Batman and Wonder Woman talk. When it is confirmed Batman has released the real Hawkgirl, Flash asks if they can just leave now but Wonder Woman persists in threatening Batman, who merely turns and walks away. Calling to him, Barry easily gets ahead of Batman, reminding him that he can't walk away from him.
Agreeing, 'Batman' catches Flash completely off-guard by flying straight into the sky above. Barry can only stare before saying, "Well...that was unexpected."
Flash is sent by Cyborg to the North Pole to retrieve a badly wounded Wonder Woman. Barry is shocked when Superman tells him that Captain Atom attempted to kill him and Wonder Woman apparently on orders from the U.S. Government and Batman. Flash apologizes to Superman before suggesting he should get medical attention as well, but Superman refuses and sends Barry off.
Barry is among the gathered Justice League with Superman as the Man of Steel announces his hunt for Batman before unveiling his growing army.
The Flash appears in his civilian identity among the gathered heroes at Oliver Queen's funeral, silently grieving for his departed friend before leaving.
The Flash accompanies Green Lantern to Congress on Superman's orders. When Green Lantern prevents the speaker from completing the government shutdown, the Flash appears, smirking and chiding him, "Inside voice."
Barry works with Hal to force Congress not to shutdown the government, sarcastically asking "Was that so hard?" when they succeed but as the two are leaving the building, they are confronted by a large group of armed forces...and Guy Gardner and Ganthet of the Green Lantern Corps.
Flash is adamant that Superman allowing Sinestro to be held on Earth in the Hall of Justice is "the worst idea ever". Superman believes Sinestro may be useful, while both Flash and Luthor believe it to be very unwise. The alien warlord admits that Flash and Luthor are wise to fear him, before saying that he and Superman are alike. This angers Flash, who snaps that Superman is nothing like him, and he calls Sinestro a psychopathic monster.
Flash is present as Sinestro relates his origins to Superman, but he is hardly sympathetic to Sinestro's past and is in disbelief that Superman may be sympathizing with him. Flash urges Superman and Luthor to leave Sinestro in his cell, but Sinestro shocks all of them by easily walking through the energy wall separating them, and stalks towards Luthor, threatening to kill him with a thought, though the Flash quickly moves between them and boats that he will smack him down faster.
Flash is shocked when Sinestro removes his ring and hands it over, still swearing that the Guardians will soon come for Superman and that they will need his help.
Though not seen, the Flash is called to Chicago to help with civilian injuries and casualties due to Despero's crash landing.
Barry reappears standing outside the Hall of Justice alongside a large gathering of Regime soldiers, Robin, Cyborg and Lex Luthor. Flash asks Cyborg what is happening when the sky suddenly lights up in a brilliant shade of emerald, and Cyborg explains that it is a blast fired from Mogo. Shortly after this, Harley Quinn attacks with Hall by blowing herself up with explosives.
Flash sees a lone Regime soldier get knocked through a window in the Hall and races over to easily save them. Barry suddenly goes limp however as the soldier is revealed to have placed a device at the base of his spine, and the soldier is soon revealed as Catwoman, who promises him the effect is not permanent and that the device was created by Batman to simply incapacitate him. Though Robin rushes to Flash's defense, he is defeated by Catwoman as well.
Flash is revealed to being held captive by the resistance in an unknown location, strapped down to a table with his mouth gagged. Harley Quinn is his captor and reveals to Barry (after much taunting) that she has been asked to 'reprogram him'. Barry is completely helpless as Harley pulls out an electrified Superman puppet to begin the deprogramming. This was Flash's final appearance in Year Two.
Barry is still bound and gagged and forced to listen to Harley Quinn as she vents her frustrations and worries over the recent events. Though Harley is called away by Zatanna, Flash's eyes widen with horror when she compliments him for being a good listener and suggests keeping him strapped down forever.