Months after Riona's revival, a Portal opens in Battleon. The player enters, but when they come out, Battleon is gone. The player searches for others, and eventually fights a battle against an unseen enemy inside a portal. Confused, the player explores more and fights strange floating Drones. After the battle is won, the player has a flashback to Warlic talking to someone in the inn about portals. Soon it is realized that someone is trying to create portals through time, and the player fights another Drone. Then a portal opens, and they are sucked through. A strange floating creature tells the player things backwards, then the player is dumped in a strange place filled with scrap metal and robot parts.
There the player meets Maxwell and Morgan, and it is revealed that the player is now in the future. After leaving the strange place, Maxwell and Morgan accompany the player out, and the player fights a boss battle against a Junkbot. Maxwell, Morgan, and the player head to find a portal back to present day Battleon.
Spawn of Carnax
Upon returning to present-day Battleon, the player finds that many monsters resembling Carnax have begun appearing and attacking all over the world in the regions of Battleon, StormFallen, and Lolosia.
Jessica Maxwell, an assassin from the future and Maxwell's half sister, Hollow Stoneforge, a descendent of Yulgar and cybernetic engineer, a Drone named 2-6-2, and the strange floating creature (now revealed to be called Cor-Demi) have come through to present day Battleon as well, and could be enlisted to help the player fight the spawn.
After 2,000,000 spawn of Carnax are killed, the player ended up in StormFallen, and fought a boss battle against a C-Rex. Once the C-Rex is defeated, a portal opens to the Future, and the group jumps in.
The player is taken to the Hatch, the meeting place of the Order of Alpha, lead by Maxwell. There the player meets Anna Darkstone, a descendant of Riona Shadowgale who shares Riona's prophetic visions. Anna wears an amulet, which appears to be an old Azru stone, probably an heirloom handed down by Riona.
There it is learned that, in the future, the sorcerer who created Carnax had traveled through time, and had learned much of the technology of the future. Using samples and DNA, the sorcerer had created his own horde of Carnax spawn, sending them to the past. Now, in the future, he had created even more of them, using cybernetic technology to increase their power. The sorcerer's name is Makkisar. Makkisar had been the host of Truth, a character who the player meets during random battles and at the Hatch when viewing the writing on the wall. Truth is an Annanuki, or Faceless, whose motives are unknown. Makkisar killed Anna's parents, and Maxwell took her in. There Anna had visions of what would happen, and that is what caused Maxwell and Morgan to head to a portal with some of Hollow's drones.
There, plans are made to kill Makkisar, ending the war in the Future and allowing time to continue properly. As the plans finish, Makkisar unleashes his latest creations.
The Last Stand
Anna senses someone coming, and Makkisar emerges to the player. He summons Carnax using futuristic technology, effectively resurrecting him. However, Anna manages to speak with Carnax, telling him how he lived on using the memories of all descendents of the Taladosians. Anna tells Carnax that he has free will, and that the one who made him such a monster - Makkisar - had no right to control him. Carnax then commits suicide by dividing his soul between all of the amulets of all the Taladosians around the world - effectively splitting him apart. Makkisar, now without a way to ever resurrect Carnax, unleashes his monsters.
Players fight a war to kill all the future Carnax spawn, fighting through the polluted waters, junkyards, and ruined cities. Eventually they are led to Makkisar, standing atop the ruined Calidon building. Anna says that Makkisar looks different, and the camera zooms in to reveal that a cloaked figure is standing there. The figure, Truth, was seen earlier by the player if the player fought random battles before entering the portal. It is then realized that Truth was the one who caused the entire series of events by first corrupting Makkisar, creating Carnax, and then heading to the future and telling the player to head through the Portal. Truth then fades away, leaving Makkisar where he was. Makkisar, fueled by Truth, attacks the player out of anger, screaming about how he will not be beaten.
Once Makkisar's HP is depleted, a cutscene triggers where Makkisar makes a final attempt to live, drinking the Carnax DNA sample, and turning into a human-Carnax hybrid and ascending further up the flaming building. Maxwell then appears in an Assault Mecha, one of Hollow's latest creations, and lets the player ride up to the top of the building with him. Maxwell then fights alongside the player against the transformed Makkisar. Once Makkisar dies, Maxwell lets the player ride his Assault Mecha out the time portal, and the player is returned to present time, ending the future war. Truth leaves Makkisar's body, and searches for a new host.