Note: This review covers both parts of "Chain of Command".
Picard is replaced as captain of the Enterprise. He, Lt. Worf and Dr. Crusher go on a secret mission into Cardassian space. His replacement, Capt. Jellico, meets his new command with some resistance from the crew. The Cardassians use theta band emissions as a ruse to lure Capt. Picard into their hands and begin brutal rounds of torture to gain the information they seek.
Why is this one of the best episodes of the entire series? Because it has plenty of action while not holding back on quality writing. We get more insight into Riker's personality and how emotional he can get when confronted with an authority he doesn't respect. And we further learn to what lengths Picard will go to defend the Federation and Dr. Crusher. How one interprets Riker is open to debate -- is he a loose cannon, a maverick? Is he unreliable? Or is he simply confident? Picard insists time and again that "there are four lights" (which is true) despite intense pain all over his body. He has a great dedication to his crew, his mission and the truth. We really see that he can be both tough and compassionate at the same time.
As with many "Next Generation" episodes, a series of moral and philosophical questions are raised. Who is the good guy and who is the bad guy here? From our perspective, the Federation is in the right and the Cardassians reveal their ruthlessness through torture and lies. But can the Federation be absolved of all wrongdoing? They crossed into Cardassian space and took covert action, clearly a violation of armistice rules.
Is the Federation plagued with hypocrisy -- claiming to be a peaceful alliance but secretly breaking laws when it's convenient? (In the grand scheme, we notice that the Federation loves to add new members to their side, as long as they stop their traditional ways of life. The striving for hegemony and assimilation is as far-reaching as the Borg, but more discreet.) Keep that in mind when watching this one... our heroes are strong and have an admirable character. But is it possible that unintentionally they are advancing a sinister or divisive objective?