Myst (series)/WMG

Myst was trashed by pirates from Mechanical
Sooner or later, they'd realize that the fortress is no longer inhabited. Some pirates might get curious.
 * Yeah, I'd say leaving a Myst linking book in an age like that is a pretty bad idea.
 * Agreed. Sure, it's locked up... by a combination that's written down in plain sight. You have to figure out the puzzle that lets you get to the combination, but the pirates just have to sail up to the other islands with their ships, land on the shore, read the answers, and put in the combination!
 * My guess would be is that Atrus merely committed the combination to memory, and when it no longer became necessary to remember (retreat of Black Pirates) he installed those pedestals so he could leave when he wanted. Also, TBP are no longer a threat. The sky of Mechanical was originally stormy and gray, and wouldn't change until all the black pirates were killed. When you link there, the skies are blue and clear.

All worlds have a linking book.
There was a past Golden Age where the D'Ni were either ridiculously creative and/or generous and taught their Reality Warper methods to other peoples. How much a particular world follows the Rules Of Index and/or takes Acceptable Breaks From Reality depends on the author.

Related to this WMG...

All Reality Warpers are D'Ni.
...and are Author Avatars having fun in their own world. Insert Haruhi jokes here.

Atrus and Catherine are liars
Word of God holds that all of the Myst games were based off of what Catherine wrote in her journals. The only games that were portrayed according to "real life" events were Myst V (based on what Richard A. Watson did) and Uru, hence the many Ret Cons. Of course, Literary Agent Hypothesis can go both ways. Atrus and Catherine could have recorded anything they wanted into their journals, effectively changing the past and there wouldn't be any way to prove them wrong.
 * What Ret Cons? Besides the Prison Age one, which was explicitly mentioned to be a shortcut for gameplay (not that that makes sense as an answer...), the only ones I can think of are those related to the rules for linking between Ages, which only apply to the Bahro and to Yeesha.

The shape of an Age's inhabitants is subconsciously affected by the shape of the Writer.
This explains why every single sapient inhabitant of every single Age that is explicitly named are Human Aliens: Atrus, Gehn, Catherine, and other Writers simply haven't figured out how to adapt Xenofiction to the Art. In fact, it may be likely that a Xenofictionally-written Age would simply fail to link, or be so alien as to be worth nothing to the D'ni other than resources. This might be why the Bahro are enslaved by the Tablet during Uru and Myst 5: the D'ni Wrote the Noloben book xenofictionally, only to find out that the Bahro were (in their opinion) only fit to serve them, and thus the whole endeavor was a failed experiment. Alternatively, The Bahro gave the Tablet to the D'ni as a peace offering, a specieswide surrender perhaps after a genocidal war. This in turn explains why Esher was so quick to write off the Bahro's form of linking as "an abomination" in Myst 5.

When Atrus dies, his body will be interred on Tay.
That is doubtless where Katran was laid to rest, and he will want to be interred with her.
 * Or, if the D'ni and Tay don't prohibit the practice of cremation, Half his ashes will be on Releeshahn with his people, and the other half with Katran.

Haven is a Pod Age at this time.
The Torus Age, meanwhile, is a Guild Classic. Spire is either a Classic or a personal Age.
 * Please Elaborate. Not all of us know what "Pod", "Guild Classic", or "Classic" Ages are.
 * Pod Ages are Ages where you link to a safe pod from where you can view the wildlife. Negilahn, Dereno, Payiferen, and Tetsonot are all pods on the same Age. Guild Classics are Ages officially regarded as the greatest ever Written. Yakul from Book of Tiana was one such, but its fate is unknown.

The Stranger is Will Navidson.
... Or rather, the protagonist of Myst and Riven is Will Navidson. In House of Leaves, it is never detailed how long Navidson disappears into the labyrinth for or how he gets out: this is because while inside the labyrinth, he discovered the Myst linking book that Atrus originally threw into the Fissure (in Myst, it is discovered by the player in what appears to be an endless black void). When he collapses into the Fissure as happens at the end of Riven, he "falls" back to the real world. This is backed up by Myst: The Official Strategy Guide, in which the main walkthrough is narrated by a man who has a camera: "Carrying case, plenty of film. If I couldn't document this place, nobody would believe it". The only flaw with this theory is that the protagonist of the Guide walkthrough starts his journey in a library, rather than in a black void. As a side note that is slightly related, the makers of The Starry Expanse Project discovered that the Temple on the first island of Riven is larger on the inside than it is on the outside. Make of it what you will (explanation starts about 9:00 minutes in).

The Stranger was drawn to the Cleft by the trapped Bahro.
A small problem with putting the exit of the Star Fissure by the Cleft is that it conveniently draws all the events of the Myst series far enough away from any kind of civilization that there is no explanation for how the Stranger, an outside observer on the trials and tribulations of Atrus' family tree, was able to enter the story to begin with. However, in Uru, an NPC in the first area mentions that lots of people had been drawn to the area, and Yeesha implies that it is her doing, with the intent to free the Bahro from their chains. (This is presumably after failing the Tablet quest as shown in Myst V, as if she'd figured out the right thing to do with the Tablet, Uru would have no plot). Given that by this point, Yeesha had all the powers of the Bahro without the humility to let them go as RAWA did at the end of Myst V, at one point the Bahro must have had the power to send out a subconscious call for help, which they undoubtedly would have used, if not before the Fall of D'ni, then definitely after. So who answered this call for help? The Stranger. What did he do at the Cleft? He found the Myst book, setting off the events of Myst and Riven, thereby reuniting Atrus and Catherine, and forging a friendship borne of gratitude that would eventually lead to Yeesha becoming the Messiah of the Bahro and setting up the plots of Uru and Myst V. Of course, there's no way the Bahro would be able to extrapolate that out, which is why they didn't try the call for help again until Yeesha set up the journey cloths and the plot of Uru.