Lean on Me Plot questions

Ok, I get the story a bit, Bad cop with a judge in his pocket.... threw out a case for a Russian Mob guy, once before. Now, what I do not get is the end... why was the Judge's nephew there, it looked like on his on free will... and if he knew his Uncle was dead or saw what was in the trunk... why not run? Or why wait to kill him afterward.. made no sense. Second, why does the Russian pay him off for killing the judge, he needed him alive to throw the case... not dead. Odd.