A Specific Theory About Nature Spirits
On this admittedly tenuous foundation, we can make a broader conjecture about these beings. Nature spirits, we suggest, are each associated with some lasting feature of the physical world which is the source of their being; they cannot stray far from it. Furthermore, they are not always active (perhaps not even always physically embodied): each is associated with some condition in the world around their "parent". This is little more than a guess, but it is a framework that not only admits both Goldberry and the giants as nature spirits but explains some of their behavior as well.
Could anything in the known cosmology of Middle-earth justify the existence of such spirits? There is indirect evidence supporting at least one possibility. As told in the "Ainulindale", Iluvatar sent "forth into the Void the Flame Imperishable" and gave the Music of the Ainur independent existence. We later read that the Elves believed that "in water there lives yet the echo of the Music of the Ainur more than in any substance". Perhaps parts of the world harboring strong "echoes" of the Music gained some measure of independent existence themselves. An argument can be made that the independent existence connected with the Flame Imperishable implies consciousness, and it would not be surprising for conscious spirits in Middle-earth to take a humanoid forms.
Because echoes of the Music were strong in water, river spirits would presumably be among the most common nature spirits, so Goldberry fits naturally into this picture. Similarly, significant features of the landscape like mountains might well hold such echoes: mountain spirits seem very natural as well. This theory even sheds light on the idea that nature spirits depend on the conditions around their "parents": echoes of the Music might naturally be strengthened when the surroundings most nearly matched the "original concept" of the parent feature. That is, the Withywindle may have been first imagined in the Music in the context of spring and summer, so in those seasons the echoes would be clearest and its associated spirit would "come to life". We know that the Misty Mountains were "reared by Melkor to hinder the riding of Orome" [Silm., "Of the Coming of the Elves"], so it is sensible that their most "natural" state would be filled with storms and chaos. Bilbo's "thunder-battle" certainly qualifies, and the Fellowship's blizzard clearly would as well.
Bombadil Himself as a Nature Spirit
With a theory about nature spirits in hand, we can finally try to apply it to Bombadil himself. In some ways, doing so weakens this essay: there is no single theory that all nature spirit proponents support, and discussing a specific one makes it possible to mistake its flaws for flaws in the entire nature spirit concept. Despite this, I believe that a fair judgment requires the theory that Tom is a Maia to be compared with a theory that is equally detailed and specific. For better or worse, that is my choice; I rely on the reader to sort the specific from the general.
If Tom is a nature spirit of the sort proposed above, we must identify the feature of the natural world that gives rise to him. It is promising that he seems bound to a small area just as Goldberry and the giants are; he states this himself in "Fog on the Barrow-Downs": "Tom's country ends here: he will not pass the borders. Tom has his house to mind, and Goldberry is waiting!" However, his country is just too varied. A spirit associated with the Old Forest would be unlikely to travel so far across the Downs, while a spirit of the Downs would be unlikely to travel deep into the Forest and beyond (in the poem "Bombadil Goes Boating", he even visits Farmer Maggot in the Shire). No single natural feature seems to define "Tom's country".
Moreover, Gandalf's words at the Council of Elrond directly state that Bombadil has not always been bound to his current lands:
"now he is withdrawn into a little land, within bounds that he has set, though none can see them, waiting perhaps for a change of days, and he will not step beyond them."
According to this, not only did Tom once range outside "his country", but the boundaries of that country are voluntary (and the reason he set them seems unknown). It seems difficult to identify Bombadil as our sort of nature spirit when he hardly seems localized at all.
Difficult does not mean impossible, however. Many facts fall into place if we conjecture that Tom is the spirit associated with Arda, with Middle-earth itself. Within "the vast halls of Ea", Arda is certainly a substantial and lasting feature, and many of the greatest Ainur centered their Music upon it. While its scale is enormous, it still seems reasonable that this "feature of the natural world" would have an associated nature spirit.
We can also guess at the condition in Middle-earth that would make its nature spirit "active". Letter #153 says that Bombadil is
"a particular embodying of pure (real) natural science: the spirit that desires knowledge of other things, their history and nature, because they are 'other' and wholly independent of the enquiring mind".
From this, we can guess that Tom was inspired to activity when surrounded by independent, individual things that he could observe, study, and interact with. This is certainly the "natural state" of Middle-earth, as it was filled with all manner of interesting geographical features and living things in the Music.
Thus, Bombadil might have become conscious of his surroundings as soon as distinct weather patterns and seas and mountains began to form, and it seems certain that he would be fully aware as soon as living things appeared in Middle-earth. All this fits well with his statement from "In the House of Tom Bombadil" that "Tom was here before the river and the trees; Tom remembers the first raindrop and the first acorn." It is not clear to what degree Tom would have existed before the Valar and Maiar arrived to shape the world, but his word "Eldest" and Glorfindel's "First" could easily refer to his status as the first "native" inhabitant of Middle-earth.
Why would Bombadil withdraw into such a small area of Middle-earth? Two reasons come easily to mind. First, his chosen country is wild and uncultivated, so both its living things and its geographical features are closer to their natural state. The orchards and fields of the Shire or Bree-land might hold less interest for him than untamed woods and deserted hills. Second, after ages of wandering, Tom may have finally decided to settle down with his favorite river spirit, and it is entirely possible that he needed to remain nearby to keep Goldberry happy and "active" in his house. It is even possible that Tom's collection of water lilies was what allowed her to live in his house, away from the river. Tom may have needed to stay nearby to tend the lilies and keep them growing through the winter.
This conjecture provides reasonable explanations for many of the puzzles and hints about Bombadil. For example, Tom and Goldberry's singing could reflect the echoes of the Music of the Ainur that gave rise to them. This would not necessarily explain the power of those songs over other beings, although it is plausible that echoes of the Music that formed the world might have power within it. (While the stone-giants are not heard to sing, their "guffawing and shouting" might not be a terrible approximation to Melkor's part in the Music. Or, Bombadil and Goldberry's love of music might not be typical.)
Another strength of this explanation is its close agreement with other known facts about Bombadil. If he is the spirit of all Arda, Galdor's statement at the Council of Elrond becomes obvious, even to one who "knows little of [him] save the name": "Power to defy our Enemy is not in him, unless such power is in the earth itself." These words fit our theory perfectly.
Tom's interactions with the Ring provide more examples. Its failure to turn him invisible might have a very simple explanation: it might treat the spirit of Arda just as it would a piece of Arda such as a rock or a metal chain. (A different and perhaps better explanation is that Tom's complete lack of desire for the Ring may have kept it from even "knowing" he was there.) As for the Ring's corrupting effects, if Bombadil's very existence stems from a desire to understand independent things in his surroundings, then there is good reason for him to have truly
"taken 'a vow of poverty', renounced control, and [taken his] delight in things for themselves without reference to [himself], watching, observing, and to some extent knowing,"
which Tolkien says in Letter #144 is the key to avoiding the lure of the Ring. We do not fully understand the twin worlds of the Seen and Unseen in Middle-earth, but nature spirits could as likely as not be aware of both, allowing Bombadil to see Frodo wearing the Ring. There is still no clear explanation for his ability to make the Ring itself disappear, but the spirit of Arda might be very familiar with gold and with the uses of Morgoth element in it. We would need a considerably better understanding of the Rings to say anything for sure.
We have already discussed how Glorfindel's word "First" applies to Bombadil, but this theory also suggests why Bombadil would be "Last" in the event of Sauron's victory. Just as "hobbits as miserable slaves would please him far more than hobbits happy and free", Sauron would eventually impose his own order on all of the wild and natural things left in the world. (Gandalf fears this sort of victory when he tells Denethor, "I shall not wholly fail of my task... if anything passes through this night that can still grow fair or bear fruit and flower again in days to come.") Tolkien writes in Letter #144 that
"Ultimately only the victory of the West will allow Bombadil to continue, or even to survive. Nothing would be left for him in the world of Sauron."
Without any independent natural things left in the world to interact with, Bombadil would no longer have the stimulus that made him "active" in the first place. Thus, as soon as Sauron's victory was complete and the last of the world fell under his domination, Bombadil's reason for existing as an active, independent spirit would be gone: he would be the Last independent "native" inhabitant of Middle-earth just as he was the First.
After all this discussion, the true explanation for Tom Bombadil remains in doubt. While we have narrowed the range of possibilities substantially, both the theory that he is one of the Maiar and the theory that he is a nature spirit seem quite viable. In the end, each person's decision rests largely on how willing they are to extrapolate beyond Tolkien's published words to guess at his true intent.
Identifying Bombadil and Goldberry as Maiar is a natural choice which fits all of the known texts well, and which leaves only a few mysteries about them unanswered. This is a very reasonable position to take, particularly for those who prefer not to be overly aggressive in inventing answers to the mysteries in the books.
Identifying Bombadil and Goldberry as nature spirits can provide ready explanations for most of the mysteries about them, but this is not surprising: if you make up an explanation from scratch, you can choose one that fits the facts. On the other hand, the specific nature spirit theory presented in this essay is based on a relatively simple premise; there is not much room to "fine tune" the theory to fit the texts. If previously unknown writings by Tolkien matched the "predictions" of this theory, it would be greatly strengthened. Even without such tests it remains quite appealing, at least to the more venturesome scholars of Middle-earth.
In the end, the only firm conclusion that we can reach is that Tom Bombadil remains an enigma; Tolkien seems to have succeeded after all. Even if Tom is never to be understood, I think that we have learned a bit about Middle-earth by searching for an answer, and I, at least, have enjoyed the quest.