Elfquest: Hidden Years takes place after ElfQuest: Kings of the Broken Wheel has culminated, which chronologically occupies the space of time between where the humans were primitive until the time of human civilization on the world of two moons.
It has a decidedly "what if" flavor and fills in many of the blanks concerning the members of the Wolfriders family who were not mentioned in the Original ElfQuest. It also retells the very origin of The High-Ones to this planet in ElfQuest: Hidden Years #9 & 10.
Hidden Years is also closely connected with ElfQuest: Shards, a sixteen part miniseries in which the elf Winnowill shapechanges into the lady Venovel and seduces both Teir and Grohmul Djun in order to exploit all the powers of the Palace and of the native animal life. Five Hidden Years issues (including ElfQuest: Hidden Years #9.5) are devoted to the telling introduction of how the Palace of The High-Ones enterred under the custody of the humans, something that Venka daughter of Kahvi and Rayek ultimately reclaimed for all elves.