Hidden enemies are special Machine Soldiers encountered in the Wii U and 3DS version of the game. There are 10 groups of hidden enemies in the game, and they appear when the player approaches them. Defeating all of them is the requirement to unlock the Dark Rodea costume.

Hidden enemies are based on regular enemies, but they have chrome plating that make them more resistant to attack, dealing out more damage with their own attacks, and giving them blue and white colors (Ion keeps calling them cute). Later hidden enemies have gold plating instead, making them even more resistant.

After defeating each group of hidden enemies, a giant crystal appears, containing a Bronze Medal for the first one, and a mech piece for the rest. Aside from the first one, hidden enemies are located on distant, lone islands.

The locations of the hidden enemies are:

  1. In Chapter 2: when traveling on the moving island to the Mendous Tree, it's on an island to the left. There are several fish enemies lined up leading to it. Once on the island, the enemy will appear when approaching the plateau. The reward for defeating it is a Bronze Medal.
  2. In Chapter 4: the island is located to the left of the island with the first warp point. The reward is a Diamond Scrap.
  3. In Chapter 6: after the first warp point, behind the island connected to the two bridges. The reward is a Giant Screw.
  4. In Chapter 7: after the area with electric walls, to the right of the island with the giant crab. The reward is an Ancient Cog.
  5. In Chapter 8: beyond the island with the octopus; it's a bit to the right, and at a lower altitude. The reward is an Adamantium Fiber.
  6. In Chapter 12: an island to the right of the first warp point. The reward is a Carbon Shaft.
  7. In Chapter 13: at the very beginning (after the fight against Rylus), the island is to the right and behind you. The reward is a X-Ray Lens.
  8. In Chapter 16: on the large island with lots of trees, behind the switch that activates the warp point, there's an island below. The reward is Ancient Parts.
  9. In Chapter 19: beyond the island with the warship; the hidden enemies are on a distant island, visible and reachable from the highest part of the island with the warship. The reward is Mysterious Parts.
  10. In Chapter 22: after the part where you have to go through the gaps in the rotating discs, it's beyond the warp point. The reward is an Old Processor.