Typical paranoid thinking...
Then can I assume you don't buy one of the premises of "The Event", where for 66 years a "secret society" that transcends the authority of the US government had been holding aliens in a mega-secret prison facility and only now a President stumbles across it and decides to undo the damage so to speak?
Yes, Section 31 has been overused in that all the series ensembles know of it according to the crossover novel series. In fact, the Hidden Frontier movie Operation Beta Shield talks of Section 31 like everyone knows about it, but not even the UFP president himself can put a stop to its illegal activities.
I'll certainly buy that the cloaking device Kirk stole in "The Enterprise Incident" was Section 31's template for the phasing cloak, but not that Section 31 ordered the mission. In Cloak
, Kirk suspects that Cartwright had his own hidden agenda, but nothing more. But if Section 31 was willing to help Archer and company undermine the activities of Terra Prime, I doubt they were masterminds behind the Khitomer conspiracy.
does make a good point that the organization is de-centralized
, so they couldn't be entirely weeded out in one fell swoop. The Bajoran Underground was able to walk amongst the general public for fifty years without being completely eradicated. And 31 has managed to stay in hiding for three centuries within a society more technologically advanced than that of the present day with their biggest secrets passed on from one generation to the next. But who is say they would remain as powerful and influential between the 25th century events of The Good That Men Do
and the 31st century?