
The Stranger might have deduced what happened by visiting various Ages (Myst was actually bigger and with more working linking books than what we see in the games) and finding more communications left by the brothers. Getting themselves imprisoned was obviously the brothers’ last action, so he might also have found the two prison books in a suspicious state, compared to the other books.
Once free, Atrus likely relocated to Rime or Myst (somewhat more comfortable than a room in K’veer without a lavatory), used the crystal viewer for signaling, and he and/or the Moiety possibly had a greater role in capturing Gehn.
Both Myst and Riven events might actually have taken weeks or even months, instead of few days as it seems in the games, and coordinated actions by more people, making an ‘actual’ reenactment more complex (and perhaps less engaging) than what could be done in the Nineties.