It is not that Tolkien is original with his stories, he is not, but rather it is the way that he uses his knowledge of European literature to create such a colourful and engaging world. His characters are not shallow, nor is he strictly black and white. Granted, there is absolutely nothing good about Sauron, but his better characters are not necessarily pure either. In this regard I think of Gandalf. He is the closest character to what one would consider a good guy in his story, but instead of calling him good, I would say that he is incredibly wise. However it is not that Gandalf is immune from corruption, it is just that he is wise enough to avoid it.
Now, Gandalf is what is called an Istari. He is one of an order of magicians who were sent by the Valar to Middle Earth to combat Sauron. The Valar chose not to physically come to Middle Earth for fear that any war against Sauron would leave the Middle Earth a desolate wasteland, so instead they sent agents in the form of the Istari. The two major ones are Gandalf and Saruman. Now, it appears at first that Saruman is a 'good guy' but it ends up becoming very clear that he has been corrupted by Sauron and has switched sides. In this part of the story Saruman is the main protagonist as he raises his army of orcs to destroy the land of Rohan. However it should be clear that if Saruman is not beyond corruption then neither is Gandalf.
When we are introduced to Theodren, King of Rohan, he is gripped with a madness and is the puppet being manipulated by Worntongue. Now, Wormtongue is dealt with quickly, but it is interesting how Tolkien's characters show mercy. While Wormtongue, a traitor allied with Saruman, deserves death, Gandalf causes them to hold back their wrath and let him flee. In that sense he is shown mercy, and this mercy is indicated because to act on instinct and give Wormtongue what he deserves is to sink to his level.
The action in this book revolves around Frodo and Sam attempting to make their way to Morder and the others defending themselves against Saruman. The idea is that Sauron's forces are to attack the lands of men (Gondor and Rohan) from the east while Saruman attacks from the west. Sauron's army is dealt with later and the main focus of this book is the battle against Saruman. However Saruman is not killed. While Pippin and Merry trick the Ents into going to war against Saruman, Saruman is not necessarily defeated (and we discover that at the end of the third book).
I want to finish this section off exploring another of the themes that runs through these books: friendship. We see the theme of friendship most clearly with Frodo and Sam. While Frodo is innocent, Sam is loyal. He refuses, point blank, to let Frodo go off by himself. Now this friendship is stretched at times, but Sam never gives up. He is determined to stand by Frodo until the end, even if it means that both of them die.
Another element of mercy that is seen in these books is in relation to Gollum. I will say more on Gollum in the next section as he is a very important character in the story. However, he is also a very pathetic and pitiful character, and while he does things deserving of death, we are reminded that he is not killed because the characters pity him. It is in this that Frodo shows friendship, even though he is not deserving of friendship, and is also very traitorous, but more on that later.