Spock states that the creature is invading our galaxy "like a virus". A Virus reproduces by injecting DNA into the cells of the host and reprogramming them to produce more viruses. This creature is a fully functional cell, capable of reproducing itself. So in point of fact the creature is invading our galaxy like a bacteria, not a virus.
The space amoeba effects were created by Frank Van der Veer of Van der Veer Photo Effects. He used coloured liquids between two thin glass sheets. Pressing the sheets at different points caused the liquids to flow around slowly, giving the appearance of life.
As they proceed, the ship encounters a gigantic zone of darkness - an area of inky blackness in space with no light in it at all, not even the light of stars on the other side. The zone lies directly on the Intrepid's flightpath. The Enterprise experiences a pull towards the zone; sensors are unable to penetrate it, so Kirk decides to take the ship inside.
Once inside it is discovered that that attractive force is growing stronger pulling the ship towards the center. A mysterious effect also starts to drain energy from the ship's systems, as well as the crew themselves. McCoy begins to issue stimulants to everybody in order to keep them going.
As they investigate the zone it seems that some of the normal laws of physics are working backwards. Normal ahead thrust from the engines makes the ship move backwards, for instance. Kirk orders forward thrust in hopes of counteracting the force pulling them in, and although this does not stop them it does slow them down. As the ship penetrates deeper into the zone something appears at the center - a colossal single celled life-form, more than ten thousand miles across. The creature appears to be creating the zone of darkness around it as some form of protection for itself.
The creature also seems to feed on energy, which is what is draining the ship and crew. Kirk orders a shuttlecraft fitted with sensors so that it can be sent into the creature. Both Spock and McCoy volunteer for the mission, even though it appears that whoever is sent will certainly not survive. Kirk agonises over who to choose - McCoy has the biological expertiese which may prove invaluable, but on the other hand Spock is better suited physically to survive the stresses involved in flying into the creature. Ultimately he decides to send Spock.
Once inside the creature Spock reports that McCoy would not have survived the shock of penetration, though McCoy finds this dubious. Spock sends back sensor readings to the ship, though his power is rapidly failing and he estimates that he has only 47 minutes left. He reaches the nucleus of the creature, detecting chromosomes inside - and indications that the creature is preparing to divide. Spock tries to inform the ship of a method to destroy the creature, but his transmissions are unable to reach the ship.
As they ponder their options Kirk muses that the creature is like an infection penetrating the galaxy, and the Enterprise is like a virus attacking the organism. McCoy compares the ship to an antibody, acting to protect their galaxy from the invading infection, and muses that perhaps that is Mankind's ultimate purpose. McCoy's use of the word "antibodies" gives Kirk an idea - a probe can be fitted with a large antimatter charge and fired into the nucleus of the creature, destroying it.
The Enterprise penetrates the creature and heads for the nucleus to plant the charge. With power levels dropping rapidly they begin to back away. On the way out they spot Spock's shuttlecraft, with him still alive inside. Despite his protest the ship locks on a tractor beam to drag the shuttle out with it. The antimatter charge detonates, and the shockwave throws both ship and shuttle clear of the creature as it is destroyed.
Then there's the idea of the creature draining energy from the ship. Fair enough... but it also drains energy from people? How does that work, exactly? It's a bit nonsensical to talk about draining energy out of people like that - is it lowering the calorific content of the food they're eating? Is it suppressing the respiration process within their cells? Or something else?
Then there's the whole "reversed laws of physics" thing. Pushing forwards makes you go backwards and vice versa? So how is it that people can still move? If your foot pushes your body forwards as normal, shouldn't that make you move backwards? Shouldn't lifting things up push them down? It's just ridiculous.
And of course there is Spocks's telepathy, which is suddenly able to work over many light years worth of distance. Even taking 400 Vulcans dying as something that would cause a giant telepathic signal, does this really make sense? Not to me. That said, the stuff with McCoy and Spock is good - seeing them competing to be the person sacrificed is a nice moment, and Kirk and Spock resigning themselves to death and taking their last moments to commend everyone but themselves is sweet. And you certainly have to give kudos to the effects, which are amazing by 1960s standards. Still, for me the bad outweighs the good in this episode.
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