The Crystal Cave is a story of the life of Merlin before he became associated with King Arthur. The book begins with a Prologue, where Merlin describes being an old man reminiscing on the past. He says that some memories are clearer than others are.

He then describes a couple having a secret rendezvous at a cave. We do not know at the time that they happen to be his parents, the Lady Niniane and Prince Ambrosius.

Merlin tells us of his early life. He speaks of his childhood in South Wales in Maridunnum, when he is about six-years-old. He has learned to find safe places to hide, because he is loathed for his parentage. No one knows who his father is. His mother will not say. The King, his grandfather, hates him for being a bastard and treats him rough, while favoring his own bastard child, Dinias, who is Merlin's cousin.

Things change, when his uncle, Camlach, returns home. Camlach's brother, Dyved, has died. Some say it could be poison. Camlach tries to pretend to be Merlin's friend, at first. Merlin has received little attention from people so he follows Camlach around like a puppy. Camlach and his grand father try to persuade Lady Niniane to marry the Gorlan of Lanascol. This would get both she and Merlin out of the way. The Lady Niniane refuses.

Merlin's grandfather, the King, is so angry at this that he storms from the hall and pushes Merlin aside. This gives Merlin a cut on the head. Merlin refuses to cry. He runs out to lie on Moravik's terrace

Camlach is pushed to a pivotal point. He finds Merlin on the terrace and tries unsuccessfully to kill him with poison apricots. Merlin innocently uses his gift, which is the ability to see the future. He sees that the fruit is black inside and doesn't eat it. He tells Camlach this. Camlach tells him to stay away from him. Merlin says this was the first time in his life that he cried.

Cerdic, who is Merlin's nurse's boyfriend, finds him in his room and tends the cut on his head. He tells Merlin that although he is named after a falcon, he should be more like a ringdove and run away from danger. He and Merlin become good friends.

Later, Camlach softens and gets Merlin a Greek tutor, named Demetrius, to prepare him for the priesthood. He thinks that sending Merlin and the Lady Niniane to the monastery would be the best thing to protect his way to the throne. This is actually good for Merlin, and he begins developing his intellect.

One day, Merlin rides out into the valley on his pony. He discovers a cave belonging to a hermit, called Galapas. He explores the cave and, while hiding from the returning hermit, discovers a crystal chamber inside. Galapas calls him out, and they begin a friendship. He becomes Galapas's pupil after that first meeting. Galapas teaches Merlin to set bones, to read the stars and to make medicines. He also teaches him about animals and plants.

Merlin's life is complicated by his ability to see into the future. He calls it 'the sight.' His nurse, Moravik, is afraid of it. Galapas begins to talk to him about it and teaches Merlin some magic. Merlin enjoys his journeys up to visit Galapas. He learns many things.

One evening, Merlin finds out that his Grandfather is going to visit the High King Vortigern, when he comes to North Wales. Galapas has insisted that Merlin must go. Merlin gathers his courage and convinces his grandfather to take him along. Merlin rides out with the men to Segontium to see King Vortigern. They arrived at Vortigern's fort in Macsen's Tower. The men who traveled with the Merlin, the King and Camlach, spent their days hunting and nights drinking and chasing women.

Merlin didn't quite understand why he was guided to go. One day, he sees his grandfather and King Vortigern wander off along the path. He goes to follow them. His servant Cerdic tries to stop him but Merlin insists. As they walk along the trail, they see a falcon chase and capture a ringdove. Both birds crash violently to the ground. When Merlin goes to investigate the birds, he spies a cave opening. The cave was an old mine. He and Cerdic go in but find nothing of interest.

Merlin returns home to his studies. One day Merlin goes into the crystal chamber in Galapas's cave again. He has a vision about things that are actually occurring. He sees and knows that his grandfather the King is dead and that he is in danger from Camlach.

Merlin rides his pony back down the hill to the palace that night. He knows that his uncle Camlach will try to use this situation against him. He tries to figure out what to do along the way. When he returns home, he climbs the outer walls and goes into his room. He packs some things to take with him knowing that he must leave. He is angry to find his friend Cerdic murdered. Before he leaves, he builds a funeral pier for him by setting him aflame. As Merlin climbs back over the wall, some men grab him. They debate what to do with the young boy. Merlin talks to them into thinking he may be a valuable hostage. They take him with them back to a boat.

Little does Merlin know that this is his best destination. The men and Merlin cross the narrow sea to Lesser Britain. The ride is horrible for Merlin. He is violently sick the entire trip. When they arrive at their destination, the two men, Marric and Hanno, awaken him. They want to take him to Ambrosius to see if he can be used as a hostage. Ambrosius and his brother, Uther, had fled England after their brother, King Constantius, was murdered.

Merlin pretends to be too sick to move. He uses his survival instincts and escapes the ship. He believes that he can go to Ambrosius alone and offer himself for work. It is bitterly cold, and he is half-naked and starved. He hides up in a barn with animals and ends up using Uther's cloak as a blanket. While he sleeps, he has a vision of a man fighting a white bull out in the field, he gets up and runs towards this scene and collapses. Soldiers found him. One of them is the owner of the cloak, Prince Uther. Uther wants to whip him for stealing, but Ambrosius defends him and treats him kindly.

Ambrosius and Uther have been building up an army in Lesser Britain. They plan to go back to Great Britain and defeat King Vortigern. Ambrosius is unusually nice to Merlin. He feeds and clothes him and lets him sleep in his room. Later Merlin is given fine clothing, and his own room.

Merlin is given a servant, Cadal. who becomes his friend. Ambrosius also provides him a shrewd teacher, named Belasius, who teaches him language and mathematics. Merlin is given the opportunity to learn many things, including engineering.

Merlin is forever curious. He gets tired of living close to the keep. One day he decides to go for a ride in the woods with Cadal. On that ride, he pushes his pony too hard and they have an accident. The return journey home must be slower. On the way back, he smells other horses and ventures off the trail. Cerdic tries to stop him but Merlin goes on. He travels deeper into the woods towards an island, where he hears chanting. Merlin realizes he has come upon a ritual. He is extremely drawn to the proceedings.

He watches in excitement. He hears a man scream as if in mortal danger. From the island, a robed man emerges holding something high in his hands. The others in the group circle him. The ritual ends and the people part ways. One of the robed figures comes toward Merlin, and he sees it is his teacher, Belasius. That night Merlin discovers that Belasius is also a Druid Priest. Belasius tells Merlin that he must study the Goddess with him, or he will be cursed. This too is added to Merlin's studies. While with Ambrosius, Merlin's character is further defined. Merlin becomes an intelligent and confident young man.

After a few years, Ambrosius and Uther are ready to make their move against King Vortigern. Ambrosius sends Merlin and Cadal back to Maridunnum to spy. The tone intensifies when Merlin meets his cousin Dinias back in his hometown. Dinias convinces Merlin to have dinner with him in a tavern. There, Dinias takes his fill of wine and food. He talks loudly about the past while Merlin tries to tell him to keep his voice down.

There are men listening to the conversation, and Merlin is captured by King Vortigern's men and taken to King's Fort, along with his mother, the Lady Niniane. This information is reported back to Ambrosius, who is ready for attack. Dinias is paid for Merlin's capture.

King Vortigern and his Queen Rowena are cruel and superstitious. Their priests have told King Vortigern that a sacrifice will make the walls of his fort stop sliding down. The walls have fallen in the past regardless of how the King has tried to fortify them. Merlin is chosen, because he has no father. His blood should be strong. Merlin's mother, Lady Niniane, unwittingly helps that belief by telling the King 's court that Merlin was conceived with an incubus.

The King and Queen decide to kill Merlin. Merlin uses his cunning and tells them that he can show them why the walls are falling. They decide to believe him and take him to the walls. He leads them to the old mine that his boy hood vision had led him to as a child. This is the cave he found when he followed his grandfather and King Vortigern down the path. Merlin figures that the fort's walls are weak because of the cave underneath them. He wants to buy time by having the King investigate this fact.

Vortigern's men dig in the cave but nothing is in the pit. Merlin begins to speak and try to divert their attention but has a vision and prophesizes that the Red Dragon Ambrosius will defeat the White Dragon Vortigern. This causes turmoil. Merlin and Cadal use the opportunity to escapes back to Maridunnum. When Merlin returns home, he goes to St. Peters. He speaks with his mother. While there, he notices a beautiful nun, named Keri, who he becomes attracted to. She plays coy with him but later asks him to cure her toothache.

Merlin describes how Ambrosius becomes King after many battles. Merlin sits upon a hill watching one battle in particular. When it is over, he walks amongst the dying and wounded on the battlefield. He finds a dying soldier and stabs him in the neck to ease his passing. This shows a colder, tougher Merlin. It shows he has become detached from the emotions of men. He now watches the movements of the whole like the prince that he is. It is at that moment that Merlin looses some of the humanity that was in the vulnerable bastard boy. He is no longer that child. Most of the battles are glossed over in Merlin's memory. Ambrosius and Uther are victorious in conflict.

During this turmoil, Merlin gets the vision that his mother has died back at St. Peter. He tells this to Ambrosius. Ambrosius wants Merlin to go to Ireland to bring back the Kings Stone and he wants victory over the Irish King. Taking the stones will cement his victory. He is fascinated with the dancing stones or monoliths that are found around the countryside.

Merlin goes to retrieve the stone. They win the battle but Ambrosius engineers have a hard time removing the stones. Merlin studies the situation and figures out how to do it. He states that it is not magic he uses but he doesn't disclose how the huge stones are removed and loaded on a barge. In England, Ambrosius dies following a battle. Merlin 'sees' this as it occurs in a vision but doesn't tell Uther, who will now become King.

Merlin and Uther both know that they do not share the same relationship as Ambrosius and Merlin had. Uther gives Merlin, Galapas's cave and mountain and Merlin returns there. Cadal has been there and has it fixed up for him when Merlin returns. Merlin has some peace, which he enjoys. During the time there, he runs into Keri, who is no longer a nun. She and Merlin kiss. Her mouth reflects the continuing motif in the story of a cave. Her kiss causes fear in Merlin. He pushes her away, and she laughs. Of all Merlin's skills it seems personal romance for himself is not one of them.

Merlin spends the rest of his time at the cave. One night, Ulfin, Belasius's old servant, rides up to the cave and tells Merlin that Uther needs him in London. Ulfin is now Uther's personal servant. Reluctantly, Merlin and Cadal return. When they arrive in London, they find chaos. Uther is about ready to be crowned at court, but he is in love with another noble's wife. It is Lady Ygraine, the wife of Gorlois of Cornwall. Gorlois has been a loyal warrior to both Ambrosius and Uther. Yet, Uther is undeterred. His behavior is erratic. He and Lady Ygraine ask Merlin for his help.

Uther, Merlin and Lady Ygraine devise a plan, where Uther and she can be together one night. Merlin knows and tells them that an important child will come from this union. They agree to this dangerous liaison. The plan involves the Lady Ygraine and Gorlois going back to their home at Tintagel early and without Uther's permission. She says she is pregnant. Uther pretends to be furious and says he is going after them. The couple makes it back to Tintagel, and Gorlois and his troops go to Dimilioc to meet and fight Uther.

Instead of going to Dimilioc, Merlin and Uther betray the warrior Gorlois. Uther, Ulfin, Cadal, and Merlin go up to Tintagel. Uther pretends to be Gorlois returning to see Lady Ygraine. They manage to get into the castle, and Uther spends the night with Lady Ygraine. They do not realize that Gorlois has been killed that night in the first battle at Dimilioc. Instead, Uther and Lady Ygraine are in bed guarded by Merlin, Ulfin, and Cadal at Tintagel.

The information of Gorlois's death causes the plan to unravel. Gorlois's men race back to Tintagel to tell his wife. Gorlois's real friends encounter Merlin and the others and fight. Merlin is injured. Cadal and several men are killed.

Uther is furious. He knows he could have waited and gotten Lady Ygraine, legitimately. He tells Merlin that he is a trickster and that he doesn't want him around. Merlin tells him that the son they are going to create would not have been the same if they had waited. Uther wants no part of it.

When the child, Arthur, is born, he is given to Merlin. He will to become the King, who unites Britain in peace and stability. This has been Merlin's goal all along.