It's no secret that Batman v Superman exists to help set up a Justice League movie. The entire "Dawn of Justice" subtitle is a hint at the future DC cinematic universe to come.
It includes multiple cameo appearances from other Justice League members, including Aquaman, Cyborg and Wonder Woman. However, it's the appearance of the Flash in the movie that is the most mysterious and perplexing.
Major spoilers for Batman v Superman below! You've been warned!
It's not exactly new information that Batman, during the film, has some kind of dream/vision in which he can be seen fighting against soldiers loyal to Superman as well as Parademons, the flying insect creatures loyal to big DC universe baddie Darkseid. In the dream, Batman walks out of a bunker into an apocalyptic hellscape and sees a massive Omega symbol (another Darkseid reference) drawn in the canyon below him. Soon, he meets up with what appears to be other resistance fighters. They've gotten their hands on a chunk of Kryptonite, presumably so that it can be weaponized and used against Superman.
That doesn't exactly work out, as it's revealed that some of the resistance fighters are actually Superman soldiers in disguise. Batman attempts to fight them, only for the soldiers and Parademons to overwhelm him. He's then captured and later executed by Superman.
Bruce wakes up from his nightmare and finds himself in the Batcave — sort of. Suddenly, what appears to be the Flash arrives on screen, but he's distorted in a white light and delivering what appears to be a message from the future. He repeatedly states "Lois Lane is the key" and that she must be saved, as a confused Bruce looks on in disbelief. He also says Bruce "was right about him" and that he needs to find "them." Then, Bruce wakes up again. You can watch the scene here (just ignore the Back to the Future part).
It's hard to make out exactly what's going on in this scene. Is Bruce's nightmare and Flash's message from the future one and the same? It would appear so, but the fact that Bruce wakes up from not one, but two "dreams" makes it all a little confusing. How could Flash send Bruce a vision of the future? What does Lois have to do with anything?
Those are questions fans don't yet have answers to. However, assuming that Flash is sending a warning to Batman in an attempt to avoid the nightmarish vision of the future in Bruce's dream, it seems that Zack Snyder may be teasing something more along the lines of an Injustice movie, rather than simply a Justice League film.
In the Injustice video game and comic book series, Superman "snaps" after the Joker tricks the Man of Steel into believing a pregnant Lois Lane is actually Doomsday. Superman plunges Lois into space, killing her, only to shortly thereafter realize he's been tricked. Metropolis is also completely destroyed in a nuclear explosion. This causes Superman to go into a blind rage, killing the Joker and declaring that no longer will he allow criminals to get away with their crimes. With other various members of the Justice League uniting behind him, Superman emerges as an all-powerful god-emperor of Earth, with Batman leading a small resistance army in opposition to him.
Flash's warning from the future seems to follow a similar train of thought. It seems Lois is the key. If she dies, Superman loses his humanity, putting him on a downward spiral to become Batman's worst fear and, apparently, team up with Darkseid.
This matches perfectly with Superman's comments to Batman in the dream, just before Superman executes the Dark Knight. Though he doesn't mention Lois by name, it's heavily implied that she was killed at some point, and that Batman may have played a role in it.
All of that: Lois dying, Superman's descent into a dictator, Batman leading a resistance, an army of soldiers loyal to the Man of Steel, comes straight from Injustice. Even Joker himself could be responsible for Lois' death in this future teased by Snyder. After all, in Injustice, Superman does at least in part blame Batman for her death, as Batman never took action to eliminate the Joker once and for all. If the Joker does kill Lois in Snyder's universe and Batman fails to stop him, it would certainly explain why Clark kills Bruce in the dream.
What's new is the whole Darkseid part of the equation. Snyder makes it clear, through the Parademons, omega symbol and Lex's comments at the end of the film, that Darkseid is on his way to conquer Earth. All that remains to be seen is if Superman will stand against him or join him.
So, is Zack Snyder teasing his own Injustice movie? Or will Batman, Wonder Woman and the rest of the Justice League save Lois and prevent Bruce's vision from becoming reality? That's the question, and one that will have to remain unanswered, until the arrival of Justice League part one in November 2017.