The sorcerers stone is in danger, and Harry Potter, although he does not yet know it, must protect it from danger. There is a couple of problems, the one who he must protect it from, is unknown. He also does not know what he is protecting.
Where is the sorcers stone?
I don't have it
Once Harry Potter gets to Hogwarts Nicholas Flamel is brought up, so he makes it his mission to find out who that is. Harry also finds out there is a box being stored at Hogwarts that is very secretive and is now curious about what is inside. Harry also learned Hagrid had a box that he would not let Harry check out.
Harry Potter follows an unidentified person into the secret hole where all his questions will be answered. He thinks it is Snape because Harry believes Snape is out to get him. After going through the magic rooms only Harry is left, leaving him to face this by himself.
Harry Potter meets Voldemort and the two fight over the sorcerers stone that Harry has. It was apparent that Voldemort needed the sorcerers stone to live fully and the only thing in his way was Harry, leaving Harry the only way to protect the sorcerers' stone.
Harry wakes up later in a hospital bed, not knowing what happened. He was eventually told that Dumbledore found Harry and Voldemort and that Voldemort was not able to steal the sorcerers stone from Harry.
Dumbledore defeated Voldemort, saved Harry, and destroyed the sorcerer's stone. Now the sorcerers stone is no longer in use, and Voldemort went to regain power somewhere else.