WARNING SPOILERS BELOW!
Warner Brothers has just posted this deleted scene onto their Youtube account. It is a short 40 second video that shows Lex Luthor in the Kryptonian ship as he's arrested by a SWAT Team. This scene may take place either during or immediately after the main battle against Doomsday with Batman, Superman and Wonder Woman as we never did get to see how or when Luthor was arrested in the movie itself. So what does the scene tell us? We already know that Luthor was using the ship for more information on the galaxy, and that by the end of the movie he seems to understand the bigger threat that is coming to Earth (which many have speculated is actually Darkseid). This scene may be the conclusion of Luthor's education in the ship.
What exactly was he learning about? That large creature in front of Luthor wasn't actually the creature itself but rather just an image of the creature, a way for the ship to teach Luthor (think of it as you would a hologram in Star Wars). We've seen this technology multiple times in Man of Steel.
The creature has been speculated to be directly linked to Darkseid and his planet Apokolips. Additionally, the creature was holding three cubes that are similar to the cube we saw in the Cyborg clip during the movie, which are most likely the mother boxes that Darkseid has used on several occasions in the comics. This would make sense as mother boxes are Apokoliptan technology. This scene appears to provide deffinite proof of Darkseid's presence in the upcoming Justice League films and it explains where Luthor got all his information from for his conversation with Batman at the end of the film.