The counter-insurgency program was a computer program Gul Dukat created in the case of a Bajoran takeover of Terok Nor. The program was designed to lockdown the space station and eventually release neurocine and activate the self destruct sequence if the rebellion continued. Unknown to Dukat, Legate Kell added another level to the program that cancelled all of Dukat's security codes if Dukat attempted to flee.

In 2371, Miles O'Brien accidentally activated the counter-insurgency program, which locked down the station and eventually activated the self destruct sequence. O'Brien and Benjamin Sisko were able to deflect the energy from the overloading fusion reactor into the deflector shields, saving the station. (DS9 episode: "Civil Defense")

Odo later rescinded the codes Elim Garak had used to move around the station freely when the program was activated, citing them as a risk to security. (DS9 novel: Hollow Men)

In 2374, Leej Terrell activated the counter-insurgency program to allow her escape from Deep Space 9 with an Orb of the Pah-wraith. (DS9 video game: The Fallen)

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