This is the only possible way for a Season 3 to happen successfully. The alien Martians will come back from space to find the human Martians inhabiting their planet and attack. The human Martians fight back, but the alien Martians override and cut off their access to Aldnoah tech/energy since they were the original creators.
This would return the series back to what it originally was. Studying the enemy super robots and using only regular robots, weapons, and creative strategies to take them down. Not only that, it would give them the opportunity to get back to some unfinished side stories like Rayet's feelings about Allusia, plus Marito and Captain Magbaredge feelings about the death of her brother.
Maybe add some story by having animosity between Klancain and Slain. Klancain has every reason to hate Slain. Slain stole Cruhteo's mech and staining its image, betrayed Allusia by collaborating with the man who shot her in the head, who is also the main leader who planned her assassination, and the one who had direct involvement in murdering his father. Let's also not forget basically usurping the Vers Empire from Allusia's control. This would make a great continuation for the series, but I know the writers will not be smart enough to think of this idea.