Dark Skies actually had an incredibly cool structure laid out which, due to the first season suffering from first season disease and not actually getting anywhere particularly fast, they never got to.
The plan was simple; one season equalled one decade.
And as the decades passed, John would rise higher in MJ-12, the war would become more public and he'd eventually realise something; we were losing.
Had they still been on air, the producers were seriously talking about doing a two hour special, New Year's Eve, 1999 that would finish, live, with Loengard delivering an address to the nation which would in essence be 'My fellow americans, for the last four decades we have been at war with an alien intelligence...'
Would have been fun:)