The storyline for Turok 3: Shadow of Oblivion picks up where Turok 2: Seeds of Evil left off when gamers were first introduced to "Oblivion" and its lackeys, 'Flesh Eaters. Oblivion is a monstrous cosmic entity that consumed everything in its path. It reigned before the birth of our universe. Invading the bodies of the living and devouring them from the inside-out, Oblivion fed on the very energy of the dead and dying. When the Primagen's Lightship was destroyed, the chain reaction it triggered as a result was so powerful that the universe as it existed was completely eradicated, and the almighty Oblivion was pushed to the very brink of destruction. For the first time, Oblivion felt pain, fear, and hate. Though totally ravaged, Oblivion survived and now desperately seeks a means to punch through the Netherscape that separates our world from the Lost Lands (a strange and primitive world where "time has no meaning"), and the Lost Lands from countless others. The last shreds of the pure energy source that created our world and nearly wiped out Oblivion are contained within the Light Burden, the bag that every member of the Turok lineage has carried. The death of the Turok mantle will signal the beginning of the end: the rebirth of Oblivion. To help it in its quest, Oblivion has utilized the aid of hundreds of its spawn-offspring. These creatures, collectively known as "The Sons of Darkness" are fanatical worshipers of their lord Oblivion. Deep within the Lost Lands, Oblivion's henchmen have a massive headquarters from where they assemble their armies, direct their operations, and center their cults, which worships Oblivion like a God. The player will eventually have to infiltrate this headquarters to destroy the scourge of the universe. It is here that their destiny will unfold, here that they must bring oblivion to that which was thought eternal...Oblivion itself.

The game begins with Joshua Fireseed (the current Turok), his sister, Danielle, and brother, Joseph. Danielle's husband has just died, and Joshua has dreams of a child that must be protected, as he is the last of the Fireseed lineage. During the night, Oblivion Spawns teleport into their home and try to kill Joshua in his sleep. He catches them and fights, but is outnumbered. He tells Danielle and Joseph to escape, while he stays behind with a bomb in his hand to blow the Spawns away, along with himself. He is apparently killed in doing so, while Danielle and Joseph drive away. They are attacked by a monster, but Adon (a female alien who helped Turok in the previous game) comes in and saves them, then teleports them to a council meeting to deal with the situation of Oblivion. They decide that either Danielle or Joseph must become the next Turok, and the player gets to choose. Danielle is a character more built on firepower with a grappling hook, while Joseph is more of a stealth-type character with night-vision goggles. In the cinemas however, it is implied that they go together in their missions.

Again developed by Bit Managers and featuring the same 2D side scrolling gameplay as the previous handheld entries and shared nothing in common with its console counterpart besides name. The game received good reviews and improved on the past Game Boy Turok games.

IGN awarded the game a score of 7.4 out of a possible 10. The IGN review notes that while Turok 3 is enjoyable, the series "has finally drifted away from its roots" and that "the series has morphed into a commonplace first-person shooter."

As well as GameSpot giving the game a 7.9 saying that "Shadow of Oblivion is successful because it concentrates upon what made the Turok franchise a best-seller instead of attempting to one-up the competition, making it in many ways the best Turok yet"