Currently, there are 6 official ARKs, 3 of which are canon and 3 of which are non-canon but WC accepted DLC's:
The Island, an island ARK. - Canon
Scorched Earth, a barren desert ARK. - Canon
Aberration, a malfunctioned, subterranean ARK. - Canon
The Center, a region-divided island ARK. - Free DLC
Ragnarok, a giant island ARK. - Free DLC
Valguero, an expansive land-locked ARK. - Free DLC
Extinction is not an ARK but rather, an area on the corrupted earth, that does house Proto-ARKs. It is part of the Canon maps. Genesis, an upcoming DLC, (Out in FEB. 2020) will further the ARK story line. And will be part of the Canon maps. Many other ARK's exist out in the ARK'verse, most are referred to as Modded maps.
The ARKs are space stations intended to house living organisms such as Humans, Creatures, and Plants. These ARKs were sent up prior to a global-level extinction event in which Element wiped out the Humans. The ARKs are powered by the Obelisks, and each ARK contains at least one Guardian. When a certain signal is given from the Earth through a strange Tek machine via a Specimen Implant, this causes all ARK to slowly descend onto earth, forming a giant seed that blooms over the Earth's wasteland, turning it into a blooming environment that once was before the global-level extinction event, and eventually rid the raw, corrupt Element that had overgrown over it.
The Homo Deus are beings created to watch over the ARKs. These beings can rarely resurrect any Humans. One did and created a new Homo Deus, A notable one, "The One Who Waits", who guides the survivor through The Island, Scorched Earth, and Aberration to Extinction via the use of Notes and Dossiers.
Proto-ARKs can be found on Extinction and are prototype ARKs. Unlike the environments that were sent up into space, Humans and Creatures can freely enter and leave the Proto-ARKs. When entering or leaving, a de-materialization effect will occur. 3 Proto-ARKs can be found throughout Extinction, two of which are operational, Desert Dome, Snow Dome, and Crater Forest. The Crater Forest was a failed experiment. This underground forest was formerly an operational, forest-themed Proto-ARK but sunk into the ground.
Spoiler ALERT!!! If you do not want the mysteries of the ARKs or the ending to this story spoiled, PLEASE DO NOT READ THIS! Everything you need to know about ARK's story before Genesis: Part I: The Island in the Sky Part II: The Destruction of the Obelisks Part III: The Call of the Corruption Part IV: Extinction's Salvation Thankyou u/diamondcreeper of Reddit for the wonderful condensation of ARK's Lore. Original post the links are from: https://www.reddit.com/r/playark/comments/cmf0xa/everything_you_need_to_know_about_arks_story/