sees it, he is surprised that he does not feel anything, as he had expected to feelsomething. He keeps look and waiting for some sensation to creep over him, but again there is nothing. Nothing except anger.

The man is angry because the rain is making him miserable and ruining his new suit and shoes, and he is angry because he does not want to be here in this place, remembering things he would rather forget.

From the corner of his eye he sees something.

Over to his right a thin, black horse was running across the ploughland towards the hill, its head down, neck stretched out. It seemed to be running on its toes like a cat, like a dog up to no good.

The man stops and the horse disappears for a bit, but the man sees the horse again as he is looking for some kind of shelter from the rain. As he continues, he sees the horse again on the ridge and then it disappears. 

The man begins making his way to the farm house located over the hill when he sees the horse again, only this time he can see that the horse has been waiting for him. The man picks up several stones and keeps walking.

This horse seems to have every intent of attacking the man, and the man naturally assumes that something must be wrong with the creature because this is not how normal horses act. Perhaps it is the infernal, never-ending rain, or perhaps the animal is sick. In any case, it seems to be stalking him.

Eventually the horse does attack:

[t]he black horse was standing under the oaks, its head high and alert, its ears pricked, watching him.... [T]his last attack had cleared up one thing.... It was definitely after him.

The man throws several stones and misses the horse; the horse keeps coming and the man ineffectually throws a few more stones. The horse keeps coming and the man finally hits him with several stones. He tells the animal that if he will stay where it is, he will not get hurt. The horse seems to understand and does stay put; the man continues to the farm where he sits in desolation, his head in his hands.

The memory of the encounter with the horse leaves him shaken and rather empty, just like whatever memories he has of this place.

We do not really know if the horse attack was real or something the man imagined, but it is clear that the horse is representative of something from his past which he was forced to confront. What that is or how this encounter will change him, we do not know.  

The main theme that Ted Hughes uses for "The Rain Horse" is Man vs. Nature. The unnamed protagonist takes a shortcut through the wood and is beset by a black horse and by the constant rain and thick trees.

The success of this last manoeuvre was restoring his confidence, but he didn't want to venture out in the open field without making sure that the horse was just where he had left it. The perfect move would be to withdraw quickly and leave the horse standing out there in the rain.
(Hughes, "The Rain Horse," Amazon.com)

Because he sees purpose in the horse's attacks, the man gives himself a similar purpose; survive. His anger at the wood and rain is unreasonable because they cannot act with purpose, but the horse can, and it gives him a reason to run, to fight back, and to escape. Without the horse to push him, the man might have ignored the rain and slept in the wood; at one point, he almost slips into hypothermia from the cold, but the memory of the horse wakes him up and drives him to action. With this purpose, the Man fights Nature and, while he doesn't necessarily win, he reaches his destination at the end.

In this short story, Ted Hughes places man against nature in a conflict that is incredibly strong in the way that it suggests man is alienated by nature. The strongest expression of this conflict is of course in the horse that pursues the man and threatens him, acting in a way that no horse really would, as it hunts the man down and becomes a physical expression of the violence of nature against man. Note how the man thinks about the horse as it becomes clear that the horse is stalking him with the intention of attacking him:

The horse was evidently mad, had an abscess on its brain or something of the sort. Or maybe it was just spiteful. Rain sometimes puts creatures into queer states.

Yet what is so interesting is that when the physical conflict between the horse and the man is over, and the man has escaped the field, the man seems to be shocked and stunned by what has happened. The narrator states that it was as if "some important part had been cut out of his brain" after the conflict. This final sentence of the story strongly suggests that he has lost something important and something that leaves him the poorer for its absence. The story perhaps indicates that the conflict with nature that the man undergoes is something that is actually vitally important to the man and his sense of understanding his place in the world. When he leaves the field, the experience is nothing but a nightmare, something that has "sunk from reality." The man once again ignores the visceral importance of nature. When he was in the field, he learned the true importance of how humans should relate to nature. Now he has left the field, he is free to ignore what he has learned, and he is left poorer and diminished as a result. This is a story that explores the relationship of man and nature, and the way in which it is vital to have a healthy respect and a true understanding of our place as humans in that relationship.