As previously stated, Man of Steel 2 will likely offer a clean slate from Superman’s last outing, but that doesn’t mean it has to ignore the events of Man of Steel completely. An adaptation of Superman: Last Son could directly deal with the fallout of the first film's Kryptonian invasion in an interesting way while also adding some new elements into the mix.
2006’s Last Son came from the minds of Geoff Johns and Richard Donner – yes, the director of 1978’s Superman: The Movie. It sees General Zod and his wife Ursa (known as Faora in the DCEU) break out of the Phantom Zone and once again attack the Earth. The twist is that they are not after global conquest this time but are trying to retrieve their son – who is living as Christopher Kent, the adoptive child of Superman and Lois.
Obviously, MoS2 would have to cut Zod out of the picture – but that could actually make it an even stronger, more layered story. That would leave Faora as a lone mother desperately searching for her son because he is all she has in the universe now that Supes has killed her husband. A romance between her and Zod wasn’t established in Man of Steel, but that could be easily rectified with some flashbacks – which would give us more of the brilliant Michael Shannon.
And if Faora isn’t dangerous enough on her own, they could always sling in another alien nasty for her to team up with instead. Maybe even Brainiac...