Secret Lab (秘密研究所 Himitsu Kenkyūsho) is a secret research facility used by Gate and serves as the location of the final stages for Mega Man X6. The Secret Lab is considered to be one of the hardest final stages in the Mega Man X series, as several sections cannot be cleared by X without equipping certain Parts or Armors.


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The laboratory is set underground near the Eurasia colony crash site, with the remains of the colony being visible at the entrance. At the beginning of the stage, the Maverick Hunters descend beneath the crash site to find large halls filled with high-tech equipment. The stages feature two statues resembling a winged demon and an angel in the background. As the player progresses, the demon statue becomes more detailed while the angel statue becomes less detailed.


During the events of Mega Man X5, Sigma tried to awaken Zero's true nature by using the Sigma Virus with the help of Dynamo. The Eurasia colony was infected with a large amount of a virus and crashed into Earth, mixing with the Sigma Virus to create the Zero Virus, and also creating the Zero Space. Fortunately, the Maverick Hunters manage to destroy most of Eurasia before it crashes, and though the impact is still severe, the damage is reduced.

Three weeks later, a mysterious scientist known as Gate investigates the crash site and discovers a piece of Zero. While trying to analyse it, he becomes Maverick, and seeks to build a utopia for strong Reploids. Gate conducts all of his work toward this goal (creating High Max, the Nightmare Virus and the Zero Nightmare, and resurrecting the previously retired Nightmare Investigators) in a secret laboratory near the impact site.


The Secret Lab consists of three stages. These stages are unlocked after defeating all eight Nightmare Investigators, defeating High Max at the end of one of the alternate paths in the regular stages, or by collecting 3000 Nightmare Souls.

Secret Lab Stage 1

Secret Lab Stage 1.

After traveling down the entrance tunnel (and losing contact with the outside) the player is confronted by several walls covered by spikes. In order to traverse this section as X, the player will need the Blade Armor, Shadow Armor, or the uncharged Ice Burst and Jumper part (found in the North Pole Area alternate path). Zero requires no additional resources, however using the Hyoroga makes the section substantially easier.

After this introduction. the level slopes down into icy platforms, and then an upward column, covered by lasers. Reaching the top leads to a jagged path with a substantial amount of enemies that ends in a door.

On the other side of the door, fire will begin to rise up from the bottom of the screen that will kill the player on contact. This trap can be avoided by clinging to the top of the wall until the fire recedes. Another fire section follows that requires a high jump and ladder climbing to avoid.

The final fire trap rises into an upward scrolling section that combines icy slopes and spiked walls which may catch players off guard, but the scroll is slow enough to allow for a cautious approach. The door at the top of this climb leads to the first boss encounter of the Secret Lab, Nightmare Mother.



Secret Lab Stage 2

Secret Lab Stage 2, first segment.

The second stage is split into two segments punctuated by bosses. The first begins in a heavily spiked corridor which must be ascended with climbing ropes. At the top, the player will come to a straight section with several levels of platforms. Though the player need only travel along the bottom section to continue through the stage, traveling along the top will lead them to an extra large Life Energy Capsule and a high number of Nightmare Viruses.

The next area is a path that winds left and right with ladders and moving platforms to advance upwards. The path is guarded by several Totem Gates with many areas covered in spikes; however, because of the winding nature of the room, it is possible to skip the right side entirely if the player can jump high enough to spawn and cling to the moving platforms on the left.

The most perilous part of the room by far is the spiked corridor at the top. One platform carries the player up to the corridor while another platform moves left and right along it, preventing attempts to jump through. The player will have to watch that the first platform does not raise them into the spikes on the ceiling while waiting for the second to move far enough away to get through. Alternatively, the player could manipulate enemies to damage them, or manuver themselves to be crushed when two platforms converge and make use of the invincibility period to qucikly dash across the spikes. Once across, the player is confronted with the door to High Max.

Secret Lab Stage 2, the infamous large gap with Shadow Armor X.

Secret Lab Stage 2, Zero's final compactor segment.

The second segment begins after defeating High Max, and is a simple straight corridor. At the end is a teleporter crystal which will warp the player to one of two different sections based on the chosen character. For X, it leads to a Nightmare Rain section like those in the Inami Temple; for Zero, it leads to a compactor section similar to the Recycle Lab.

X's section is notable for featuring an extremely wide gap that normally requires an Air Dash to cross. If the player is using the Shadow Armor, which lacks this capability, they will need the Hyper Dash part (fittingly, found in the alternate area of the Inami Temple) to dash jump from the bottom of the left platform across to the right one. The player can also extend their jump distance with use of the charged saber swing or Giga Attack to make it easier.

If the player is not using any armor at all, they can cross the gap using Hyper Dash in the same manner, or by "hovering" across with alternating activations of the Magma Blade and Ground Dash weapons via the pause screen.

Zero's section features three compactors which require various amounts of crouching to pass through safely. The player must be careful to avoid taking damage while ducking, or they will be forced to stand up and potentially be fatally crushed. The final compactor reaches all the way to the floor and so it must be avoided by clinging to the sides of the platforms and continually Wall Kicking while waiting for opportunities to advance. During this section, the player will be assailed by Group Jets. Making use of the Yammar Option as a shield can help to avoid contact damage and a fall into the pits.

Regardless of the chosen character, the following section is a straight pathway to the final confrontation with Gate.

First Segment




Second Segment

With X

With Zero


?????? (Stage 3)

Teleporters to the Nightmare Investigators Commander Yammark (right), and Blizzard Wolfang (center).

This stage is also split into two segments. The first segment begins with a downward corridor with spike-lined walls. At the bottom, the right side opens up to a room with Energy Capsules and eight teleporters, each leading to a battle with a Nightmare Investigator. As is traditional for the series, each one must be defeated for the player to advance. Note that in this area, all of the Investigators are set to Level 4 irrespective of the player's Hunter Rank.

After all eight are defeated, a ninth purple teleporter will appear at the top. This teleporter leads to a short section brimming with enemies - at the end of which awaits the final confrontation with Sigma.





  • The Secret Lab music is a remixed version of the X-Hunter Stage 2 music.
  • The Secret Lab contains many of the original hazards from the stages occupied by the Nightmare Investigators. The Amazon Area is the only one not referenced in the stage's hazards or enemies.
  • The Stage Select Screen pinpoints the stage's location on what looked like the Australia continent, but as the pointers in the Mega Man X6 map aren't accurate (North Pole Area being on what appears to be southeast of Asia and Amazon Area on the Pacific Ocean, for example), it is more likely to be on the south of Asia, where Eurasia crahsed.
  • The extra large Life Energy Capsule in the second stage of the Secret Lab is the only one present in the game.
  • The Secret Lab is one of only two final stages in the Mega Man X series (the other being the Zero Space in X5) that can be accessed without completing all of the main stages first.
  • Infamously, the Secret Lab is the only stage that requires X to use optional Armor, Parts, or Weapons to complete it.
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