The design of the Luminoth is clever. When you think about it, Samus is helping some moths turn their lamp on.
Upon entering the Agon Wastes, probably one of the first things you'll spot is the large structure on top of the main area, with some giant caterpillar statue on its side; scanning this statue will have your data suggest that it may be a warning to travelers. Turns out that the statue represents Amorbis, the game's first real boss, meaning it was really a warning for the player.
There are some things about the Space Pirate base that don't make sense at first glance. For example, we know that the Pirate operation on Aether was a very stealthy operation, so stealthy to the point that the Pirate expeditionary force on the planet was relying on a single transport ship making occasional supply drops for them. It seems impossible that such a major base on Aether could have been constructed with only a token force and one ship. But consider a few things:
Echoes features the Space Pirates utilizing some kind of Flashy Teleportation technology to move around the planet. Corruption also sees some Pirates warping, but it is explicitly Phazon-based; the teleporting we see in Echoes is that a beam of yellow light appears, and a Pirate emerges from it.
Near the end of the game, once you obtain the Light Suit, Samus can also warp around the planet using beams of yellow light. The log book data indicates she is making use of a Luminoth Portal Network.
There are two Luminoth Keybearer corpses in the Pirate base.
The metal gate leading into the base is stated in the scan data to be made of Luminoth materials.
The Dark Beam is found in the base, and it is not a Pirate weapon. It is kept in a secure, isolated chamber, and scan data indicates the Pirates found it and were studying it.
Conclusion: the Space Pirate base on Aether was a Luminoth base that they moved into upon making planetfall. With an infrastructure already in place, suddenly the fact they only have a single transport supplying them makes much more sense: it would only need to carry weapons, computers, and other makeshift portable gear instead of the kind of heavy construction equipment necessary to build a base from scratch. After getting themselves situated, they must have discovered the existence of the Luminoth warp network and found a way to breach it.
Why did Samus go to Aether? Because the Federation received a distress signal from its marines. Why were the marines on Aether? They were chasing a signal they intercepted from the Space Pirates. How did they intercept that signal? Dark Samus destroyed the Pirates' jamming apparatus. What does Samus do once she's on Aether? She unlocks, defeats the guardians, and generally frees the way to all the most Phazon-rich areas on the planet. Echoes entirely worked out in Dark Samus' favor, as Samus dealt with the Ing while Dark Samus just strolled right behind her and snarfed down all the Phazon it could find. And if Dark Samus had not done these things, Samus would not have gone to Aether, which means the Ing would have succeeded in replacing Aether with Dark Aether, bringing about the total destruction of all life on Aether and the Luminoth. After Samus won, Dark Samus decided to step it up and just take over the Space Pirates so she could use them as Mooks.
The only time we ever see the Ing possess a deceased creature is when it controls the Federation troopers at the beginning of the game. After that instance, there's never any indication the Ing even have this power. But there is evidence they can possess non-living matter when it comes to the robotic sentinels in the Sanctuary Fortress. So what we see in the beginning of the game aren't Darkling troopers, but their Darkling Federation power suits. This even explains the zombie-like jerkiness of their movement.
The game takes place on Aether, a planet that is known to be a rogue body. This planet, alongside all others visited in the Prime saga save Hunters, suffered the impact of a Phazon meteor. Because Phaaze supposedly always targets a planet for invasion, it's very possible that poor Aether wasn't meant to suffer the impact, it only crossed in the way to an actually targeted planet! Poor Luminoth...
Not necessarily; a rogue planet once discovered would be easily characterized in terms of its vector, and such characterization would be necessary if anyone intended to visit it ever again — if you don't know where it's going, how do you expect to find it when you wish to return? Targeting it with a Phazon meteor then becomes an elementary problem in ballistics, such that hitting it on purpose is many orders of magnitude simpler than doing so by accident. (This remains true even when you consider influence from other bodies of significant mass; projecting the last known vector of the rogue planet would lead to any such bodies close enough to exert gravitational influence, and knowing the mass of all bodies involved would allow further extrapolation to find the planet's current position and vector. NASA has done this for decades with interplanetary probes; for the Galactic Federation, or whoever, to do so, would be so utterly trivial that their astrogation equipment would probably do it automatically.)
Samus gets the energy transfer module just a few rooms away from U-Mos. The Ing's victory and total destruction of Aether was only minutes away at best.
The Space Pirate lore scans are partial Fridge Horror and partial Fridge Hilarity, depending on your level of schadenfreude. Reading them shows how the Space Pirates got in over their heads by unknowingly interfering with the Ing, in what was supposed to be a simple Phazon investigation on a seemingly-abandoned planet. Then they met Dark Samus, who began stealing all their precious Phazon and broke their cloaking device. Then they were discovered by the Galactic Federation, who began pursuing them as well. This culminated in Samus herself coming to Aether and finishing off their operation. It seems like literally everything went wrong for the guys, and none of it was even their fault.
On the Pirate Homeworld in Corruption you can find a scan referring to the events of Echoes. It pretty much sums up the situation: "Surely, we are cursed."
On the other hand, we have the crew of the GFS Tyr. After following a single Space Pirate frigate to Aether, their ship crash-landed thanks to the chaotic atmosphere. They then discovered that the Space Pirates had an entire compound built, and thus prepare their own encampment to take them on. However, this encampment was overtaken by Dark Splinters, who slaughtered and strung up every last one of them. Like the Space Pirates, none of them could have predicted this outcome and it's hard to imagine being in such an awful situation.
The concept of Ing possession is the usual Brainwashed and Crazy trope, but a step worse. The Ing seem to fully replace the minds of the Darklings they possess, effectively ending their consciousnesses for the course of the possession. While it's written in lore that Ings can freely abandon their Darkling hosts, this never happens in-game, meaning the last memory of any monster Samus kills is of their own violent possession. Most wildlife on Aether doesn't even understand what the Ing are due to how recently they entered the ecosystem, making it all the more unfortunate.
Luminoth lore scans show that the Luminoth could become Darklings as well. It details how many Luminoth had to slaughter their friends and family - women and children included - or else they would be killed in turn. Additionally, many corpses of Luminoth can be found who killed themselves in order to prevent possession from the Ing in their last moments, even mangling their own bodies in order to keep the Ing from using their corpses (as seen with the fates of the GF marines).
In the official Q&A for Echoes it was revealed that the Ing's minds are like highly-intelligent sharks. Imagine your spouse or child suddenly turning into a raving beast bent on murdering you because of some dark fog appearing out of no where.
The Emperor Ing being mutated by Phazon shows you how powerful the substance is in comparison. Even the mightiest of the Ing, masters of shapeshifting, are at the mercy of Phazon.