In a game about a covert-ish organisation, it’s quite natural to look at other covert-ish organisations and what they might be up to. Torchwood kept themselves hidden from UNIT, MI5, MI6 and the police, and were indirectly responsible for the Children Of Earth situation. The three families behind Miracle Day were even m ore secretive, and are still out there, working on Plan B.
(Probably not this Plan B, but you never know.)
A conspiracy, governmental or criminal, could be mixed up in world-spanning (or bigger) threats, as well as smaller plots closer to home. They might be working with alien technology, with aliens, or for aliens.
They could be aliens themselves, taking over the world or pursuing another aim, passing for human or going unnoticed and keeping Silent.
Or something else paranormal might be going on. Or even nothing directly paranormal - they just cross paths with the PCs another way entirely and don’t take kindly to them...
Whatever the case, conspiracies and covert-ish organisations can cause a lot of trouble. Even a small one can have scarily dedicated followers, and a large one could have spies, assassins, security forces, expert thieves and hackers on speed dial. Even without any super-tech or powers, a black ops team could be more than many groups can handle.
Example: The Committee
A number of alien artefacts have gone missing, inactive ones stolen from known collectors and active ones taken from official safe storage. Worse, alien artefact dealers have gone missing. Someone is employing highly skilled thieves to collect everything connected to one particular extraterrestrial group. Items, information - they had quite a trade going on with the early Torchwood Institute a hundred years ago, so there are various bits and bobs all over, but nothing too dangerous... so why the sudden interest? And what if there are still members of the species living unnoticed on Earth? Who can they turn to for protection?