This song is about Kirk's relationship to the Enterprise, tracking his freaky devotion to a piece of spacecraft through his various incarnations. Kirk once said he didn't need any woman, because he was already marriedto the Enterprise! One could scarcely hope for a more brutally weird and Freudian articulation of late-twentieth-century anxiety about mechanization.
Anyway, this first verse comes from "This Side of Paradise", an episode from the original run of Star Trek. In it, the Enterprise crew stumbles upon a planet where all the inhabitants have been infected by spores that turn them into hallucinating, mellow-yellow hippies. The entire crew of the Enterprise decides to join them in transcendental harmony, and Kirkglue-addled with sporesbeams his entire crew down.
Unfortunately, the transporter acts up, and Kirk has one of his little temper tantrums. The adrenaline from his tantrum kills the sporesforcing a moment of quiet clarity upon him. As he wanders the deserted Enterprise, he realizes it isn't much more than a huge hunk of metal.