"Why did you call that creature 'Dark Samus'?" Twilight asked once everyone had stopped laughing. "I mean, I know it looked a lot like you-"
"Because it was basically Metroid Prime wearing my Phazon Suit," Samus interrupted, causing several of the mares to gasp. "When it pulled the Phazon corruption out of my power suit, it also got a sample of my DNA. So when it recreated itself somehow in Phazon elsewhere, it did so in my image, along with abilities based on my own."
"Not a pleasant sight," Spike pointed out. "Especially since it just wouldn't stay dead."
The mares shuddered at the sound of this, though the fillies and draconequus looked all the more eager for details. Seeing their faces, Samus chuckled. "Alright," she replied. "At any rate..."
Once Samus had comforted Spike for not being able to get any Phazon to help him adapt to Dark Aether, the pair continued their exploration of the base. Not far down a new path, Samus found a new beam weapon system. The Dark Beam was a weapon designed by the Luminoth to use the Ing's own energy against them. However, according to the specs, the Luminoth had never figured out how to create a dark energy generator small enough to fit in a hand held weapon. As a result, the Dark Beam relied on an ammunition system, and replenishing ammo by absorbing dark energy from the environment, or collecting Dark Ammo from storage containers. Samus' own power suit was unable to fully analyze the Dark Energy the weapon was based on, and as such could not use its own energy generators - which fueled the Power Beam and other Chozo tech - to supplement it.
As many of the various devices scattered around used Dark Energy to activate, this proved most useful for Samus. Unfortunately, beam cannon based weapons were not compatible with Spike's armor, as his only beam weapon was his breath. However, given just how powerful his breath was, Spike was content to rely on that and his melee combat abilities.
Returning back to the entrance chamber of the Space Pirate base, Samus discovered that the portal to Dark Aether the Pirates had been using could be energized with Dark Energy. Firing the Dark Beam at the rift, the portal opened, letting the pair through to the shadowy world.
...
On the other side of the portal, Spike and Samus found themselves in a wide open chamber. One of the keys to the Dark Agon Temple - a red oval gem surrounded by two rotating black rings - was in plain sight. Nearby was a small amount of Phazon, not enough for Spike to easily consume, especially as it was outside any safe zone.
Nearby was also a glowing sphere of light. Samus' scans revealed it to be a beacon, Luminoth tech that, when activated, created a temporary safe zone. It was apparently designed after the war had strained Luminoth resources, and the Crystals that made the permanent Safe Zones could no longer be built.
Manipulating some Luminoth tech platforms, Samus and Spike were able to continue onward through the area. In the next chamber, there was a large puddle of Phazon...and two full canisters.
"Mom...I have an idea," Spike said carefully. "If it doesn't work, I'm going to need you to pull me back into the Safe Zone here as fast as you can."
"Keep your tail in range, then," Samus replied. "No Grapple Beam, remember?"
Nodding, Spike grabbed the two canisters and hurled them against the large pool of Phazon on the floor and wall opposite, charging after them. As the Phazon erupted and he entered the field of the explosion, Spike disengaged his suit's energy shields.
Samus flinched as she heard him roar in pain and the sizzle of Dark Aether's atmosphere on his scales...but both noises quickly faded. When she could see clearly again, all the Phazon was gone, and Spike had changed.
The change wasn't as drastic as most of the ones he'd gone through. His scales had changed to much darker shades of purple and green - contrasting much more vividly against the white and gold of his armor - and his teeth were a brighter white. The white of his sclera had turned red, and the slitting of his pupils had become more pronounced. The spines along his back were also slightly sharper. "Spike?" she asked as his armor reactivated the energy shields.
"I'm okay," he replied. "But...my energy's dropping a lot slower now."
Curious, Samus scanned Spike.
Adult Spike - Dark Mode
By absorbing Phazon mixed with Dark Aether's atmosphere, Spike has created a partial adaption to Dark Aether's atmosphere. It appears Spike can shift back and forth between this mode and his normal state. This adaption has reduced the energy drain on his shielding by 90%. His high stamina allows him to function at the equivalent energy levels of your suit with maximum energy levels.(1)
Samus disengaged her scan. "Well, that's going to be helpful," she murmured as they headed for the next chamber. The explosion of Phazon had also killed the Warrior Ing that had been in the chamber with them, so they went unmolested.
As the path further on led to a narrow passage, the pair were forced to split up, Samus continuing forward and Spike trying to loop back around from the other side.
"Splitting up?" Rainbow asked worriedly. "In a world of shadows, darkness, and poison filled with monsters made of living shadow, the whole thing looking straight out of a horror movie...and you split up?"
Samus and Spike glanced at each other. "Well...when you put it that way..." Spike began.
"Sounds even more fun!" Samus replied eagerly.
Twilight chuckled. "Something tells me you'd greet a zombie apocolypse as a fun challenge full of free targets."
Spike glanced towards Samus. "So...does BSL count as that?"
Samus shrugged. "Close enough."
"BSL?" Luna inquired.
"Our last mission before coming here," Samus explained. "We won't say anymore, so put the sign down, Pinkie."
Pinkie giggled as she lowered her 'Spoilers' sign.
After a time, Samus found another Luminoth beam weapon system, this one designed to use Light Energy. The generator issue the Dark Beam had was also present with the Light Beam, and her suit could no more generate Light Energy than Dark, so she was still forced to rely on ammunition. However, she did discover that the use of one type of ammo to destroy an enemy would cause it to release energy of the other type, which her Arm Cannon could absorb to convert into ammunition.
Seeing that the chamber was open air, Samus figured Spike had taken the opportunity to explore from the sky, so she decided to go back to the chamber of the portal back to Aether to wait for him.
However, by the time she got to that chamber, she found Spike waiting for her where she had seen the Key before. "Done exploring already?" she asked.
"It's a lot easier to explore this world flying," he replied. "Much of Dark Agon is open air, although the Temple Grounds and Dark Temple are sealed by the Keys. Speaking of..." Opening a compartment in the chest plate of his armor, he set out three Keys - two red, one pale green - along with several expansions for Samus' Power Suit. "Picked up some stuff for you while I was flying...but this key looks different."
Collecting all the pickups, Samus blinked. "This one is a...Sky Temple Key," Samus explained. "Apparently, it's one of nine to open the path to the Energy Controller in the central area of Dark Aether, equivalent to the Great Temple in Aether where U-Mos stands guard."
Spike blinked. "Huh. No wonder it was contained inside an Ing. Speaking of, found out eating the Ing replenishes me like this nearly as efficiently as Phazon...though they don't taste very good."
Samus shrugged. "Then don't eat too many of them," she instructed. "If they don't taste good, they probably aren't good for you."
"They weren't," Spike murmured to the listening audience.
Everyone was silent for a time. "Spike?" Samus asked.
"...I'll explain later..."
(1) This means that Spike's normal stamina is equivalent to Samus with all Energy Tanks. Also, the damage reduction from the atmosphere for Spike in 'Dark Mode' is equivalent to Samus with the Dark Suit.