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At the beginning of the episode, Kirk, Spock, and three redshirts are on the surface of a world gathering mineral samples. Kirk smells something that reminds him of a past encounter and sends the redshirts to investigate, telling them to scan for "dikironium" and to shoot any clouds they might see. The cloud appears and quickly encompasses the redshirts; two die immediately and one later on the Enterprise, from lack of hemoglobin. (This gives the corpses a striking bluish appearance, the accuracy of which I have no idea.)
Kirk believes that this is the same cloud-like creature that killed about half the crew, including the captain, of the Farragut eleven years ago when Kirk was a young officer. He's determined to stay and find the creature, despite the fact that the Enterprise is due to rendezvous with another starship to pick up perishable vaccines for a world in dire need. None of Kirk's senior officers believe the cloud is living, let alone dangerous, which does not deter Kirk.
Kirk leads another landing party to find the creature. He orders Ensign Garrovick (son of the late captain of the Farragut) to take two security guards one way, while he and two more guards go another way. He orders all of them to shoot the creature at full power immediately upon sighting it. The cloud approaches Garrovick's team; Garrovick freezes a moment in hesitation. By the time he fires, the other two men are dead.
Kirk, Spock, and McCoy debrief Garrovick aboard the Enterprise. Garrovick cannot provide any evidence that supports Kirk's belief that the cloud is a living creature. When he reveals his hesitation, Kirk relieves him of duty and confines him to quarters. Then he refuses to hear Spock and McCoy's opinions, telling them to put them in their reports. He also refuses to leave the planet, despite repeated reminders about the medical emergency.
Up to this point, Kirk has been very terse in his discussion of the "creature" with Spock and McCoy. He has referred them to the reports from the incident with the Farragut. Spock reads the reports and goes to ask McCoy about the human problem of "obsession". He and McCoy devise a plan, although we don't realize their planning at first.
McCoy goes to Kirk's quarters and tells him that he should lighten up on young officers, and that it's only natural to freeze up in a high-pressure situation. Kirk assumes McCoy is talking about Ensign Garrovick, but McCoy replies he's talking about the young Kirk, who froze up in a similar situation. Kirk admits he still feels guilty, but refuses the parallel with Garrovick. McCoy raises the bar and tells Kirk that he believes his obsession with the creature has gone too far, and he's considering writing a medical log entry concerning the captain's mental and emotional competence. Of course, to do this, he needs a command-level witness...which cues Spock's entrance.
Kirk's behavior during this scene is interesting. First, he's irritated at McCoy's nosiness, and is a little rude, calling the bridge instead of replying to McCoy's conversation. McCoy's medical threat puts him on the defensive, of course. We know that losing his command is his biggest fear. But when Spock enters, he seems to realize that Spock is someone he can "out-logic" and he pulls himself together and presents a very rational front.
Spock follows the recommended procedure in regulations when confronting a senior officer with irrational behavior, which includes scripted conversations. I had never thought about this, but it makes perfect sense - you don't want a junior officer failing to act concerning a crazy superior just because he doesn't know how to start the conversation! Kirk tells him to forget the regulations, and presents a logical case to Spock: if this creature is the same one that he encountered eleven years ago, then it's very deadly, since it killed hundreds of people then. This planet is light-years away from that planet, so the creature is capable of traveling great distances. Its primary "food" is hemoglobin. All of these facets make the creature a grave threat to inhabited Federation worlds. Spock is taken in by the logic and Kirk's more rational manner, and he and McCoy have their fears assuaged.
Shortly later, Chekov reports from the bridge that the cloud is leaving the planet and heading out into space. Kirk orders pursuit, but the cloud is moving so fast that they are forced to travel at unsafe speeds. Ensign Garrovick comes to the bridge to ask to return to duty during the emergency, which conveniently allows him to witness the subsequent events.
Eventually, the cloud slows down and Kirk orders a phaser attack. The phasers pass through the cloud with no effect. Photon torpedoes also have no effect. The cloud reverses course and approaches them, passing through the deflector shields. It is able to enter the Enterprise through an open exhaust vent. Several people on the ship are killed by it before all the ventilation ducts are sealed and reverse air pressure is applied.
Spock has also come to the conclusion that the cloud is a living, intelligent creature, since it turned to attack them. He also speculates that the creature is somehow able to be "somewhere else" when phaser fire and other weapons are applied. As he points out to Kirk, his hesitation eleven years ago made no difference, since his phaser wouldn't have harmed the creature. Kirk is in no mood to hear it. He orders radioactive waste from the impulse engines flushed into the ventilation system to try to chase the creature out. I have to wonder just how safe this is for the crew!
Spock goes to Garrovick's quarters to try to convince the ensign that he was not to blame for recent events. Garrovick is feeling too much self-pity to listen. However, this scene puts Spock in Garrovick's quarters just when the creature finds Garrovick's open vent - the ensign had accidentally broken it open earlier in a fit of anger. Spock orders Garrovick out and proceeds to block the vent with his own body until reverse air pressure is applied in the cabin. Kirk, McCoy, and Garrovick are ready to plan Spock's funeral, but he is unharmed - his blood does not have hemoglobin.
Kirk takes Garrovick aside and points out that the ship's phasers had no effect on the creature, so there's no way Garrovick's phaser could have, even if he hadn't hesitated. And even though Spock had pointed out that this applied to Kirk eleven years ago, we can see that finally sink in here. Garrovick and Kirk implicitly absolve each other of the blame for the past attacks.
The creature leaves the ship and heads off into space. Kirk feels like the creature's smell now indicates "home", which he believes is the planet upon which the Farragut encountered it. They head for that planet. Randomly, Spock announces that the evidence suggests the creature is intending to spawn, and that it would do so by dividing into many smaller creatures. What evidence? How does he know it's going to spawn, and how would he have any idea how it would spawn? This is an annoying statement which seems to exist just to provide additional justification for Kirk's obsession.
Since ship's weapons are ineffective against the creature, Kirk plans to kill it using antimatter. He will beam an antimatter bomb to the planet's surface and lure the creature there with a vat of blood. (Apparently the planet is not inhabited, since the subject is never mentioned, even though the bomb should blow away part of the planet's atmosphere.) Garrovick volunteers to help. The beam-up will be tricky, since they will have to wait until the last moment and beam up during the explosion.
When they beam down to the planet, for some reason they decide to move the bomb to some distance away from the beam-down point. Why? I don't know! This leaves the blood unprotected, and the creature arrives and absorbs it. Now they don't have bait.
Kirk immediately decides that he will be the bait, by waiting really until the last minute to beam up. Garrovick thinks Kirk is intending to sacrifice himself and tries to knock Kirk out, but Kirk whacks him back and tells him to stop being an idiot. The cloud approaches and they beam out just as the set off the bomb.
It takes a long time for them to materialize on the Enterprise. This is a classic teamwork scene, as both Spock and Scotty apply their expertise to the transporter while McCoy waits breathlessly. Once Kirk and Garrovick are safely aboard, Kirk takes Garrovick to his quarters to tell him "tall stories" about his father.
This episode has a lot of good points, mostly relating to the idea of Kirk being obsessed. The reason for his obsession is well laid out with his past on the Farragut, and it's clear that he's bottled up his guilt for years. His initial reaction, which is to close up and barely speak to Spock and McCoy, is very obviously defensive.
The episode shows once again how much power a starship captain has. Kirk puts off the rendezvous for the vaccines, and even considering his obsession, apparently has no real worries that he will get in trouble for this. Even though Spock and McCoy begin following the official procedures for dealing with an irrational captain, it's not clear how effective the procedures would be or how quickly they could resolve a dangerous situation.
The connection between Kirk and the young Garrovick is nice, even if the parallels in the situation are a little too obvious. There are obviously families with military traditions in Starfleet, just as there are families with traditions in the armed forces today. It's easy to see how Kirk might take Garrovick under his wing - too bad we don't see Garrovick again.
I'm not sure the timelines concerning Kirk's history all work out. Here we learn that he was an officer fresh out of the academy eleven years ago on the Farragut, and the elder Garrovick was his first captain. That would make Kirk a lieutenant, I believe - I can't remember if it was explicitly stated in the episode. Going from lieutenant to captain in eleven years is quite an achievement! Plus, in "A Private Little War" we were told that Kirk visited the planet in that episode fifteen years ago. Something seems off here.
I do have some issue with the logic of the episode. The creature could apparently allow energy to pass through it - the phasers appear to be some kind of light energy. We aren't really told what photon torpedoes are, although the name again implies light energy. Spock says it's because the creature can somehow not be there at the time the energy goes through. Then the creature goes through the deflector screens.
If the creature can pass through things (or allow things to pass through it), why can't it enter the Enterprise by going directly through the walls? Why can it be confined to the ventilation system? This seems like a bit of a plot convenience.
Spock also speculates that the creature moves itself by using gravitational fields. What on Earth could he mean by this? If he means a ballistic trajectory, such as shooting a cannon ball in the air and letting gravity pull it back down, then there's no way the creature could maneuver like it did. What else could Spock mean? Does he mean the creature can create a warp field in spacetime like the Enterprise does? That doesn't make sense, just because the Enterprise is never described as using gravitational fields to move. This is an example of some technobabble on the series - usually it's not so bad.
This episode had one of the highest death tolls of any I can remember. We know of five redshirts that died on the planet, plus more crewmembers that died when the creature invaded the ship. This should give Kirk more to obsess about!
I always find it amusing when antimatter is used so readily as a solution to problems in science fiction. Obviously, the Federation has come up with a way to more easily produce antimatter than we can today. Today, the description on Wikipedia states that antimatter costs about $300 billion per milligram to make, which would be about $8.5 x 10^15 per ounce. A little prohibitive for a weapon!