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They track down the Constellation in a planetary system where all but the two inner planets have been destroyed. The Constellation looks like it's been seriously beaten up; the bridge is destroyed. Kirk leads a boarding party consisting of Scotty, McCoy, and damage control crewmen, prudently leaving Spock on the Enterprise, just in case.
On the Constellation, they find that life support is barely functioning, there are no shields, and the phaser banks have been depleted. The ship is completely void of crew. Eventually they find the ship's commander, Commodore Matthew Decker, in auxiliary control. Decker is in shock; McCoy gives him some drugs while Scotty plays back the last captain's log for Kirk. Apparently the Constellation was tracking some kind of huge planet-killing device; they attacked it, but the retaliation of the planet-killer was overwhelming.
Decker recovers somewhat and tells Kirk that he had no choice but to order the crew to abandon ship; he had beamed them all down to the third planet when the transporter malfunctioned, stranding Decker aboard. This leads to one of the most tragic and affecting exchanges in the episode as Kirk says, "Matt, there's no third planet." Almost in tears, Decker replies, "Don't you think I know that! But there was!" He goes on to describe how after he beamed down his crew, the planet-killer began destroying the planet; the crew desperately asked to be transported back aboard, but with the broken transporter, all Decker could do was watch and listen as they died. Decker is obviously completely destroyed by the events, feels reponsible for his crew's death, and feels guilty for still being alive.
At times I think the actor playing Decker over-acts a bit, but on the other hand, the circumstances certainly warrant a lot of drama on Decker's part. I can't imagine being in his shoes. And his strong feelings here set up his motivations for his actions later in the episode. Not only does he want revenge for his crew, but he wants to fix what he sees as his mistake in not destroying the planet-killer.
Kirk orders McCoy to take Decker back to the Enterprise for medical care. He orders Scotty to get the Constellation ready to be towed. At this point, the planet-killer arrives and attacks the Enterprise. Decker exercises his authority according to regulations and forces Spock to relinquish command of the Enterprise. He orders an attack on the planet-killer.
The planet-killer is the source of the subspace interference, so communications between the ships is cut off. Kirk is blind and helpless on the Constellation, and there's no way he's going to sit still for that! He orders Scotty to call up a miracle and get the Constellation's sublight engines working. Kirk himself fixes up the viewing screen in auxiliary control (with the help of one of the damage control crewmen) so that he can see what's going on. This is a nice touch, because it gives Kirk a lot of credibility when we see that he's actually competent to do this sort of thing.
Meanwhile, the Enterprise is having absolutely no success in its attack on the planet-killer. Spock keeps recommending a strategic withdrawal, far enough to escape the subspace interference so that they can warn Starfleet Command. He points out that the planet-killer's hull is made of neutronium, which is strong enough to defeat all of their weapons. Decker refuses. The planet-killer eventually damages the ship enough to knock out the warp drive.
By the time Kirk gets the viewer working, he's aghast to see the Enterprise fighting the planet-killer. Scotty gets the sublight engines going, and incidentally has also gotten one phaser bank recharged. This sequence is one of the first real showcases of Scotty's "miracle-working" abilities, and demonstrates why Kirk relies on him so much. Kirk decides to attack (what else would you do with a crippled ship against an insurmountable enemy?) in order to distract the planet-killer from the Enterprise. This works, but instead of retreating, Decker orders renewed attacks.
Communications between the ships is restored, and Kirk is aghast (again!) to find out that Decker is in command. He relieves Decker of command on his authority as captain of the Enterprise. This is apparently within regulations, since Spock goes along with it, but appears to be unusual. Spock and Kirk then arrange a mutual withdrawal from the planet-killer and a rendezvous of their ships.
Spock orders Decker to sickbay, but Decker hijacks a shuttlecraft. Despite the urgings of Spock and Kirk to return, he pilots his shuttlecraft right into the maw of the planet-killer. The shuttlecraft explodes inside the planet-killer. Sulu detects a slight drop in power from the planet-killer, and Kirk realizes Decker might have had a good idea.
Kirk gets Scotty to rig a self-destruct button with a 30 second delay for the Constellation - he intends to send the ship into the planet-killer and blow it up. When Scotty beams back to the Enterprise, the stressed transporter system malfunctions. Fortunately, Scotty's there to fix it. Kirk sets the Constellation on course, pushes the self-destruct, and calls for beam-out. But the transporter breaks again, and Scotty must do a quick fix while Spock counts down the time Kirk has left. Kirk is beamed out just in time. The Constellation's explosion successfully destroys the planet-killer.
This episode has always been a favorite of mine, although I can't articulate exactly why. It's one of the more suspenseful episodes, because the threat is very dramatic, and there's no hope of help. I also enjoy the MacGyver-nature of Kirk and Scotty's work on the Constellation, which is making something out of virtually nothing. There's a nice rapport between Kirk and Spock, even though they spend most of the episode on separate ships. When Kirk puts Spock back in command of the Enterprise, I get the feeling that it's because there's no one else that Kirk would rather have in command, not just that Decker is obviously unstable.
The contrast between Spock's interaction with Kirk and his interaction with Decker is very interesting. With Kirk, Spock plays off of Kirk's ideas and even shows concern for his captain, such as when Kirk proposes to send the Constellation into the planet-killer. However, with Decker, Spock is the consummate, completely unemotional Vulcan. He performs his duties precisely, albeit putting in as many recommendations for retreat as possible. Leonard Nimoy's portrayal of this constrast is commendable.
McCoy also has a memorable scene, when he pleads with Spock to somehow remove Decker from command. He knows that such an action would be right, but as usual he is frustrated by the fact that they must follow the letter of regulations. And we are offended along with McCoy when Decker "asks" McCoy to leave the bridge.
The only real detraction in the episode is the attempt to shoehorn in a bit of political commentary. Kirk concludes that the planet-killer is a doomsday machine: an ultimate weapon built only as a threat, but never intended to be used, because it would likely destroy both sides in any war. First, Kirk discusses how old-Earth hydrogen bombs were such a doomsday weapon. At the end of the episode, Kirk brings it up again, with the idea that they used one doomsday weapon (a hydrogen bomb) to destroy another. This is laying it on a little thick.