Dismissing his trip back to his time, Shadow went after Mephiles to ask if he was behind the destruction in their future. Avoiding the question, Mephiles tried instead to get Shadow to join him. When Shadow refused, Mephiles engaged him in battle instead.
Predicting Mephiles' intentions, Shadow, Rouge and E-123 Omega made their way to Dusty Desert to stop Mephiles from collecting a Chaos Emerald, but they were too late. Mephiles tried once more to make Shadow join his side, but Shadow saw through the lies of his adversary. Seeing it was futile, Mephiles covered the entire arena in darkness for a final battle between them.
Mephiles Phase 1
When the battle begins, Mephiles melts into the ground, becoming Shadow’s shade. The player cannot hit Mephiles when he’s in this form, though Mephiles cannot attack either. Instead, he leaves his tiny underlings to keep you busy. These mini monsters are the key to defeating Mephiles. To beat Mephiles, the player must store up enough Light Cores to fill your Action Gauge and activate Chaos Boost by destroying the minions. The monsters swarm the player throughout the battle, glomming on if the player let them get too close. If enough underlings grab the player, they explode and deal heavy damage. Attacking the under-lings one at a time with Homing Attacks takes too long. Instead, wait for the underlings to surround you, then use Shadow’s Spin Kick to eliminate several at a time.
When the player activates Chaos Boost, the underlings retreat and Mephiles takes his corporeal form. At this point, the player can physical damage Mephiles. When the Action Gauge is completely drained, Mephiles becomes a shadow again and the player must reﬁll the gauge by destroying the underlings. Mephiles attacks with purple energy balls that grow in size as they chase you through the arena. The best course of action is to dodge these, though it is advised to close the grab between Mephiles and the player. The player can damage Mephiles with Homing Attacks, but he will often slip away. Freeze Mephiles for a few seconds with a Chaos Lance and move in for a Chaos Attack.
For the second phase of the battle, the player controls Omega while Mephiles remains in his physical form for the entirety of the ﬁght. Mephiles will try to hide behind his horde of underlings, so use Omega’s Lock-On Shot to keep the distance and target multiple enemies. As long as Mephiles is directly in front of the player when in the targeting phase, one of the shots is likely to hit him when the player release the attack button. After the player strike Mephiles one or two times, he sends forth his underlings to dive bomb Omega. When this happens, run around the arena to avoid getting pelted by the mini-monsters as they smash down to earth. Mephiles also fires the purple energy balls at Omega. These balls move in a straight line, so as long as the player keep moving, none of them will hit Omega. Do not try to target Mephiles during this attack, because as soon as the player slows down to line up a shot, he will blast Omega with a purple ball. Keep repeating this until Mephiles is defeated.
Mephiles Phase 2
When the battle begins, Mephiles unleash its brutish first form. Use this time to skate around the arena and pick up Rings. The player will need as many as they can scoop up, because when the monstrous manifestations of Mephiles smash the player with giant ﬁsts and burn the player with the laser. Mephiles’s monstrous form is anchored to the ground and only appears in the four corners of the arena. The player has to go to it in order to defeat it and earn Light Cores to initiate the Chaos Boost that can bring Mephiles down. Mephiles’s laser stretches the length of the arena, so either run from it or jump over it and close in on Mephiles while it’s busy ﬁnishing the attack. When the player see Mephiles arms rise into the air, move back or in toward the center of the monster’s body to avoid getting hit. Mephiles’s weak spot while in this form is the light core it reveals when opening its maw. Jump up and use a Homing Attack/Chaos Attack to slam into the core. When Mephiles' beast is defeated, multiple Light Cores are released. Keep repeating the attacks until the Action Gauge is full enough to start the Chaos Boost.
Once the player activate Shadow’s Chaos Boost, the colossal manifestations vanish and Mephiles is forced to attack Shadow in its normal physical form. Once this happens, it starts unleashing purple energy balls to streak across the arena. Rush around the arena in a zigzag pattern to avoid the blasts as you zero in on Mephiles. After the player chip away half of Mephiles’s health, it uses multiple dopplegangers to distract the player from the real enemy. All Mephileses can release the purple blasts, making it harder to dodge and zero in on the central ﬁgure. To ﬁnd the real Mephiles, the player needs to hit the ﬁgures with Chaos Lances. The false forms disappear when struck with the Chaos Lance. Mephiles moves quickly if it is difficult for the player to zero in on it with a Homing Attack and do damage, use Chaos Lances to temporarily freeze it. As soon as Mephiles cannot move, hit it with a Chaos Attack. As soon as the Action Gauge runs out, Mephiles rises out of range and brings back the monster forms. The player must then attack them to earn light cores and start the process over again. Keep repeating this pattern and Mephiles will be defeated.
- In the "Mephiles Phase 2" battle, a glitch occurs if the player uses Chaos Snap on Mephiles repeatedly and instantly when he is flying above Shadow, which will cause the ground to turn black and the player to fall into a bottomless pit.