Toxic fumigation was an emergency failsafe protocol in the Silurian city designed to protect it from infection.
When toxic fumigation was activated, all Silurians were to return to their hibernation chambers before a toxic gas was released into the city, killing anything left not in hibernation. Once this was done, the entire city would go into shutdown. (TV: Cold Blood)
After Restac's coup in 2020, the Silurian leader Eldane offered to initiate toxic fumigation to buy the Eleventh Doctor, Ambrose Northover, Mo Northover, Elliot Northover, Amy Pond, Rory Williams and Nasreen Chaudhry time to reach the Doctor's TARDIS and escape. Concerned for his species, Eldane felt that the Earth was not ready for the Silurians to return and that only those insane enough to follow Restac would die from the gas. Agreeing with Eldane's sentiment, the Doctor set the hibernation chambers to awaken the Silurians in a thousand years and ordered the humans to spread the word.
On the Doctor's signal, Eldane activated toxic fumigation, causing Restac's warriors to immediately return to their hibernation chambers. All the humans but Nasreen and Tony Mack took the opportunity to flee to the TARDIS as toxic gas filled the Silurian city and all but Restac returned to hibernation. As the Doctor, Amy and Rory prepared to enter the TARDIS, they were confronted by Restac who had stayed out of her hibernation chamber and was thus fatally exposed to the gas. Restac took a shot at the Doctor before succumbing to the effects of the gas and dying. However, Rory took the shot to protect the Doctor and was killed instead. (TV: Cold Blood)