After entering Earthend, Ton, Chin, Kan and Hatapon scout the area before them before noticing a purple lake right in the center of the land. They approach it to find their surroundings slowly transform into a purplish tint to find a castle-like structure out of the lake, a blood-red moon rises. They stand their ground, hoping that they would return home soon, but an escape is nowhere to be found. The castle door opens and they venture inside. They climb to the top and find a standing Mahopon. The only thing that looked odd about the Mahopon was the four demonic horns protruding from the sides of its head.
The being spoke to them to tell she was one of the ten remaing ancient Akumapatapons, ancient servants of the Underworld who broke free from the Dark Lord's control. Most of them were killed by the Akumapons, but as this happened, it bought time for the ancient Patapons to escape Earthend in order to survive. The Patapons then evolved into what they are now.
The being called herself, "Aurapon" and told that, together, they would finally be able to fulfill their prophecy to travel back down the Underworld and finally destroy all evil. She changed the Patapons into Akumapatapons to grant them power for their long journey. They must defeat the evil Black Mask and find the remaining 9 generals in order to assault the Underworld, save their original bloodline, and finally restore peace in Earthend.
- The Uberhero returns, but this time everyone joins in, including Meden.
- You can now use the tribes, Zigoton, Karmen, and Akumapon, after beating "The Black Mask" the Accursed Ones.
- As opposed to the Uberhero (now called Shadowhero), there are also 7 Generals who were created by the Accursed Ones to command the Corrazen Scourge. There are 5 Archdemon Heroes that guard the Arch Mask's Lair (The Black Mask's Castle).
- You travel between the 3 dimensions: Earthend, The Normal World and the Underworld. Mater is not present in Earthend, but is on the normal world. To gain access to the Underworld, you must first defeat all seven generals, must have saved at least 3 Archdemon heroes to their real forms, and must have obtained the key from The Black Mask after he has been defeated.
- The Shadowhero can obtain new masks (similair to the Patapon 2 in which you can change the hero's masks) however these will not affect its class nor its Rarepon type.
- Many of the old monsters return into new "Corrupted", "Demonic" and "Accursed" counterparts with difficulty increased respectively on their new types.
- Queen Kharma and Ormen Karmen return as an ally and enemy respectively, Queen Kharma would be revived into a Shadowhero form which broke free from the "Black Mask". While Ormen Karmen returns as a far more powerful form that has his hatred with the Patapons into a greater level after what happened in Pata-pole palace. He returns in the form of "Ormen Corrazen"
- 4 new units are available: The whip carrying Flagellupon, the magical spell-javelin carrying Volupon, the floating magicians Sagapon and the spell-blade wielding Malidictipon.