Many prokaryotes encode CRISPR-Cas systems as immune protection against bacteriophages. During infection, jumbo phages evade DNA-targeting CRISPR–Cas immunity by physically protecting their DNA inside a viral nucleus-like structure. However, phage mRNA remains vulnerable to RNA-targeting CRISPR–Cas systems (e.g. type III) when exiting the nucleus for translation. In Serratia the type III-A accessory nuclease is required for defence against the jumbo phage PCH45; however, the mechanism of protection is unclear. Here we solved the crystal structure of the accessory nuclease revealing that it is a hexameric protein of the NucC family that binds cA3 for activation of the endonuclease by promoting coordinated dsDNA cleavage in vitro. Using plasmid targeting and phage infection assays we demonstrate that NucC is activated upon the targeting of invader RNA, which results in destruction of the bacterial genome. Consequently, immune infected cells initiate their own death, thus providing clonal bacterial population protection by suppressing the phage epidemic. Overall, our data indicates that type III CRISPR-Cas systems overcome the inaccessible nature of jumbo phage DNA via abortive infection. Bioinformatic and experimental data showed that type III jumbo phage immunity is widespread and can be elicited by accessory DNases as well as RNases.