This is by far the simplest of all questions...and it occured to me while reading ultimate fantastic four.
Have a war raging under everyone's noses between atlantis and also the inhumans.
Have namor, a prisoner of atlantis released from his toombe and wish to exact his revenge for the loss of atlantis by first rebuilding it and then plunging taking out the whole surface.
the fantastic four would have to intervene with johnny siding with the inhumans with reed and sue and namor siding with ben.
Ultimately it leads to a big fight where namor takes on blackbolt and the fantastic four have to deal with the inhumans and atlanteans/or ressurected atlanteans trying their best to take on the surface world.
it ends up being that maximus the mad has used this all as a big distraction from his real aim to take blackbolt away from his kingdom and declare himself king and he is the one that released namor and fed everyone the wrong info.
it's a great story that tells of times before humans became the dominant species on this planet. It also gives johnny sometime with crystal that would lead to his girlfriend getting jealous and making her become galactus' next herald when he comes. It also highlights sue's relationship with Namor and how reed's jealousy gets in the way.
Most of all it gives us a big comicbook fight between two heroes that wouldn't normally get one, Namor/Blackbolt which would be awesome.
it'd probably have to be 2 and a bit hours to get it done but bring some real depth to the franchise' world.
Finally to conclude, we could see either the mole man or doom yet again picking up some devices from both civilizations ready to use in their next scheme.
that's how I would DO IT.