One of the Internal Affairs detectives tells Cragen that they understand why he doesn't like them, since it was IA that made him take down his own mentor. This is referring to the events of
The Blue Wall (1991), when Captain Cragen was in command of the 27th precinct. Cragen's former commanding officer, Peter O'Farrel, who held the rank of Deputy Chief at that point, had been accepting bribes from the mob for years, including back when Cragen worked with him. He took bribes and helped cover up numerous crimes including drug and weapon smuggling, prostitution of underage girls, armed robbery and murder. O'Farrel knew that IA suspected that a high ranking member of the department was dirty and that they were closing in on him, so he attempted to frame Cragen by having someone hack the NYPD database as well as Cragen's financial information to make it appear that Cragen was taking bribes. This worked at first as Cragen was relieved of duty and indicted on charges of tampering with evidence, receiving bribes and embezzlement. The only way Cragen was able to clear his name was by wearing a wire and getting his old mentor and friend to admit what he had done. IA made Cragen do this, his choice was to either "rat" on his mentor and friend or loose his rank, job, pension and freedom.