Speculation on my part:
Whoever the villain was fighting in that brief scene, they weren't human. They were wearing metal helmets. They may be Klingons, like the helmet wearing ones from ST2009 deleted scenes.
If so, maybe Botany Bay was recovered by the Klingons who experimented with the crew to work on fixing their ridges and only 1 superman survives and it isn't Khan. Then due to the horrors of Klingon experiments, he gets bitter about his exile from Earth and goes back for revenge. Old Spock sacrifices himself at the end to save Kirk and Young Spock.
Whoever the villain was fighting in that brief scene, they weren't human. They were wearing metal helmets. They may be Klingons, like the helmet wearing ones from ST2009 deleted scenes.
If so, maybe Botany Bay was recovered by the Klingons who experimented with the crew to work on fixing their ridges and only 1 superman survives and it isn't Khan. Then due to the horrors of Klingon experiments, he gets bitter about his exile from Earth and goes back for revenge. Old Spock sacrifices himself at the end to save Kirk and Young Spock.