When Marc Laidlaw posted Epistle 3, commonly read as the plot he intended for Half-Life 2: Episode 3, he included references to events which were happening within Aperture during the Seven Hour War. He described scientists attempting to prevent the Combine forces from taking the Borealis, the research ship that was constructed in the drydock in Old Aperture.

I think this plot point might make for an interesting game. Imagine GLaDOS commanding an army of portal-gun-wielding robots to defend the enrichment center from waves of alien commandoes. The game could be a hybrid between Portal's puzzles and Half-Life's combat. What do you all think?