Aether: To the Sanctuary
"So...if I understood what you were talking about earlier right," Twilight began, "there's only one more major area of Aether you haven't told us about yet, right?"
"That's right," Samus agreed. "The last area we needed to retrieve all the planetary energy for was the Sanctuary Fortress region. U-Mos had quite a bit to say about that..."
Returning to the Grand Temple, Samus and Spike saw that energy now streamed between it and Torvus Temple, showing their progress in that regard. U-Mos was staring up at it in awe. "The Temple of Torvus glows with energy once more," he marveled. "Only one temple remains without the Light of Aether." Turning to face Samus and Spike, he began to explain. "You must travel to our fortress, high in the cliffs." He showed a holographic image of the area in question. "You should seek knowledge within the temple itself before attempting to invade the Ing Hive, the shadowy reflection of our Sanctuary."
"Sounds like a plan," Spike agreed.
"What will we have to face in there?" Samus asked.
U-Mos sighed as he called up an image of a quadrapedal mech unit. "The Fortress is guarded by machines of our creation. Once, they were our allies...but the Ing now command them. They will attack you on sight."
"That'll be interesting," Spike murmured.
"Pretty sure machines aren't edible, even for you," Samus teased.
"Which means I'll need to be careful about how many hits I take," Spike pointed out. "I won't be able to restore myself by eating, like I have elsewhere."
"Do not lose hope," U-Mos encouraged. "Our goal draws ever closer. May the Light of Aether be your guide."
Nodding, Spike and Samus turned, making their way to the Sanctuary Fortress.
The Fortress itself was as astounding as the image had made it out to be. The full extent of Luminoth tech was on display, showing just how advanced the civilization really was. The entire place was automated, tending to itself without any observation. And the actual Fortress was suspended atop a massive rock pillar, connected to the rest of the mountains only by a narrow bridge.
However, there was one thing Spike noticed right off the bat. The majority of the Fortress was internally contained. There was very little of it open to the air, which would make maneuvering for him somewhat difficult.
Halfway across the bridge, the pair were attacked by several Pirate Commandos. While Samus focused on charging across the bridge to get a better attack angle, Spike leapt off it, taking to the air for combat. The two pronged attack proved too much for the pirates, who were too used to being able to outnumber and surround their targets, not being surrounded themselves.
Once those were dealt with, the interior of the Fortress proved even more impressive than the outside, especially the sheer size of the power generators and energy control systems. The sheer scale was beyond anything they'd ever seen in the Federation, and easily on par with what Samus knew the Chozo had been capable of...though the Chozo tended to prefer to use multiple smaller power stations rather than a single massive one.
Spike was forced to detour through open areas of the Fortress for most of their explorations, as there were quite a few narrow tunnels too small for him. However, they were able to meet up at the entrance to the Sanctuary Temple grounds, where they discovered that the Ing, in addition to remotely controlling the various mecha that the Luminoth had built, could actually possess them. While this made them more dangerous and lethal in combat, the added vulnerability to light and heat resulted in the smaller possessed mechas becoming so much slag before Spike's flame breath.
Within the Temple itself, they found the recorded message of the Temple's last Sentinel.
"Hear the words of O-Lir, last Sentinel of the Fortress Temple. May they serve you well. This used to be a great Fortress, a safe haven for our people during the war. It also holds portals to the Ing Hive, the heart of their dark tribe."
"And that's safe how?" Spike murmured under his breath.
"Hush," Samus scolded.
The message continued. "During the war, I built a number of mechanical sentinels to join me in battle. They were made to fight the Ing, and fight them they did...for a time. One by one, the Ing corrupted them. Now they attack with no mercy. Many went to Dark Aether with their Ing Masters."
"Calling it now!" Rainbow called out. "Hive Guardian's a giant robot!"
"Do you mind?" Samus demanded. "We were in the midst of relating a noble warrior's last words."
"Kill bad guys, save us all, sorry I screwed up big time," Rainbow summarized. "How close am I?"
"No reason to be disrespectful of the legacy of someone who gave their life for their people and world, Rainbow," Spike chided gently.
Rainbow's ears went flat against her skull. "Sorry..."
"At any rate..." Samus continued.
The message continued. "Expect them when you are in the Hive. The Ing like to use them as guards."
Spike watched as Rainbow mightily resisted the urge to say anything else.
"How come ya didn't encounter them anywhere else, then?" Applejack asked. "Ah mean, if they're so tough, why not use 'em in Agon or Torvus?"
"They probably weren't hermetically sealed," Twilight pointed out. "Computer circuitry is exceptionally delicate. Without proper protection, a single mote of dust can fry an entire machine if it gets in the wrong part."
Spike scratched his chin thoughtfully. "That's probably why we only saw the Darkling Mechs in interior portions of the Ing Hive..."
Nodding, Samus continued relating the message.
"The Ing will protect their home with great ferocity. In all our battles, the Hive has never fallen."
The message then updated Samus and Spike's translator modules so they could access the last color of hologram interfaces.
"If only I could join you...redeem my fallen honor in battle. But, my time has passed. Good Luck. May the Light of Aether show you the way."
With the message over, Spike and Samus turned to explore the Temple, to find a way to attack the Hive's core.
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Dammit, Dash!
I thought you of all ponies would have more respect for those who LOYALLY gave their lives to save others! 
Another enjoyable chapter. Good job.
Loved that line
6408816 To be fair, she did paraphrase him almost exactly. Just wait till it's her turn.
6409012 Still feel like smackin' her upside the head for how she did it.
6404975 You'll need to scan it before you can hit it with a super missile, otherwise it's not going to target the blue patch. If it hits anywhere else, it will just bounce off.
I'm going to admit it. Since I never played these games I have no idea what these Space Pirates and Pirate Commandos and whatnot look like, so this whole time I've been picturing them like classic swashbucklers and buccaneers straight out of the Caribbean, but equipped with various forms of 1950's style laser pistols.
6409027 Fair enough. I can agree she needs a whack.
6409150
Anthromorphic crawdads.
Solution to fighting things you can't eat: kill things you can and bring them as rations.
I don't know what your excuse will be for Samus losing her powers in the other games, but I have a suggestion for the transition from Metroid 2 to Super.
Specifically the animated joke around the four minute mark. Sorry it isn't just the animation, but for some reason nobody's uploaded it by itself.
6409150 Actually, what Fluttershy said earlier is pretty accurate. They're crawdad people. I will say that your idea is a lot funnier, though.
6409220
I actually have a very easy explanation for what happens to her abilities between 2 and 3. Which I'll reveal at that point.
Please show the annoyance of Rezbits.
They super missiled me too many times...
(Oh right, can't forget about blocking craved dark beam....
)
I can't wait to see the ponies reaction to the death of everyone's favorite Prime bounty hunter Rundis. at least i think everyone likes him. most of the people I see on the internet seem to love him.
6409247 I wasn't really expecting you to go for it. I just think the joke in that video is absolutely hilarious. Maybe it could be a suggestion from the mane 6? Something along the lines of "What got rid of your power ups next, a rock to your shoulder?" Anyway, I'm looking forward to the rest of this fic. Keep on writing these awesome stories!
Time for one of Samus's biggest boss battles size wise. Still all that delicate circuitry Twilight mentioned means if Spike can make some scratches on a mecha's armor, he could leave lots of vulnerabilities for Samus to exploit.
6409217 That's only obvious if you've played enough video games like Minecraft.
WIse move.
Goodie...
Yep.
I see.
Nice.
Very most likely, but be a bit more tactful, please.
Makes sense.
Here we go, we're about to face the Ing Hive.
Closer and closer to the finale.
It will be interesting to see the interaction betwixt the two as Phazon poisoning sets in.
Spike should definitely try anyway, they might be close enough to gemstones to count.
6409247 how many games of metroid are there? Are you gonna recount them all? Where is Riddley? Didn't he came to equestria, so why hasn't he appeared yet? What IS he doing while spike and samus talk all day long?
SOOOOOO MANY QUESTIONS!!!!!!!
Into the hive
!...
6421508 Calm down calm down. Take it one at a time.
6602550 speaking of hive, changlings vs spike anyone?
Dang it, Rainbow! I know it's predictable but-
Rude Dash
6408816
Eeyup.