Flash sees the darkness of this universe and wants to change it for the better.
He goes back in time only he makes thing EVEN worse. Learning from his mistakes he knows how to correct and when he goes back he alters the timeline once again to create a brand new one.
Timeline 1 -> Current BvS/JL timeline with emo Superman and murder Batman all leading up into Superman turning bad with troops like in the Injustice timeline. Flash goes back in time to change it.
Timeline 2 -> Flashpoint timeline, Bruce dies instead of parents, Aquaman and WW at war with each other, Superman held prisoner by the government. Flash goes back in time to fix everything again.
Timeline 3 -> Invasion in MoS happens but the world engines are placed in inhabited zones, invasion clears with no casualties. Superman becomes more confident in himself as a hero. Batman doesn't lose Robin yet and isn't unhinged, more hopeful about humanity and Gotham in general. Batman and Superman meet under amicable terms. Things are going into normal territory.
aka the night is darkest just before the dawn (of Justice).