A reputable judge uncovers a citywide crime syndicate, and is kidnapped. The judge was a friend of Jack's father, so the cop is obligated to send a few hundred men to their graves in order to make things right. Before long, all hell breaks loose, so Jack and his K-9 cohort Shadow must take on a powerful mob in the fight of their lives to break the city’s spiral of betrayal and corruption. In the end, the judge is murdered and although Jack gets the killer, goons of a high-ranking Russian crime lord named Blanchov get the judge's files. Jack's girlfriend Ruby is murdered by Blanchov and although Jack never retrieves the files (they were likely Hennesey's files from the first game), he goes after Blanchov for revenge. Jack kills Blanchov, but gets no satisfaction out of it knowing that Blanchov is just a highly placed puppet that can easily be replaced. Having lost Ruby, Jack has nothing to really live for anymore. Also he claims that whoever is responsible has him Dead to Rights as they got the files and he ended up with nothing.
Source: Wikipedia, "Dead to Rights II", available under the CC-BY-SA License.