Story
This section contains spoilers which could ruin the game for you if you have not played it before, or have not yet reached the end.
It could be argued that the story of Myst starts with Atrus trapping Gehn on Riven by throwing himself and the Myst book into the Fissure [see: Book of Atrus]. However the events of Myst takes places some 20 years after the events detailed in The Book of Atrus. In that time Atrus and Catherine have gotten married and had two sons, Sirrus and Achenar.
Atrus sought to teach his sons the ways of The Art and to respect the Ages and their inhabitants, however he failed to teach his sons this respect. As a result Sirrus and Achenar trampled through the Ages, plundering them ripping apart the civilizations within before burning the Descriptive Books, breaking the link to the Age for good. Atrus knew that greedy travellers might arrive one day so he wrote to Prison Ages and placed them in his library on Myst Island, in hopes to trap the traveller. He never thought it would be his own sons who would be trapped.
Sirrus and Achenar conspired again their parents. Telling their mother, Catherine, that Atrus had gone to K’veer she Linked there to find him, not seeing Atrus there she assumed he had returned to Riven after all these years and so Linked to Riven. The sons removed a page from the Linking Book in K’veer that lead back to Myst then tricked Atrus in Linking to K’veer trapping him back in the room his own father had imprisoned him in several decades before. Having trapped both of their parents, Sirrus and Achenar decided to venture into the Ages that Atrus had forbade them from going to thus trapping themselves. Unknown to Atrus the Myst Linking Book he had dropped into the Fissure had arrived on Earth and into the hands of “The Stranger”. The Stranger Linked to Myst and found the place empty, by following clues left around Myst Island and the few surviving Ages of the destruction wrought by Sirrus and Achenar, The Stranger was able to discover the truth and free Atrus.
Dissapointed with the betrayal of his sons Atrus burns the Linking Books to the two Prison Ages apparently destroying the Link for good. It is the start of a long friendship between Atrus and The Stranger, a friendship that will involve The Stranger going to Riven to confront Atrus’ father.