Feedback [SPOILERS] (Solutions) Fixing up plot holes in the story.

So, I noticed quite some plot holes in the story, and I would like to make some suggestions to make it better. I imagine the Devs already have stuff in mind, but I'll try my hand at it anyway.

So, first off, we have the destruction of Earth. It seems that for most of the races this makes sense, but for the Novakid it goes completely against every grain of their species to join the protectorate, or to even care about it. (Not to mention if you actually did join the protectorate, you'd likely have scientists flocking to study you at every turn, being that you are the only Novakid in the universe to stay at one place for years on end)

As such, we see that there must be other story options. There are a few ways to implement this, them being race specific, or selectable with character creation, but the Ark should only be used in the Earth Protectorate Questline.

But enough said about that, this is about the main story as we have it.

SO... Earth's destruction is a plot hole in itself.
One, why did the Ruin target only Earth?
Two, How did the Ruin do it, since it is currently sealed away with no way to get to it (No way in, no way out) as seen by us needing to do the main questline to access it.
Three, How are you and Esther the only protectorates left? Shouldn't they be all over the galaxy?

To resolve these, I have the following:
One and Two: These could be solved with a great reveal at the end, at the final face-off with the evil girl at the heart of the Ruin. She could applaud you for opening the gate and doing exactly what she had intended to do. She could explain that she found out, thanks to Esther, that the Protectorates had with them a special relic that held some of the Ruin's powers, which they were using to create the matter manipulators (Notice how the Ruin is able to open portals and teleport monsters to you during the battle). She had thought that this was one of the relics to open the door, and went to retrieve it. However, when she took it out of its location, the ruin seemed to grow immensely in power, and attacked those who had held it for so long through the power of the relic. Sadly, this destroyed Earth, but she figured it was for a better cause. The Protectorate were holding back Humanity after all, forcing them to serve the other races, instead of ruling them.
Three: Simple. Not all, but only most of them were destroyed. It should be mentioned in the opening scenes "Wow, who would think that graduation day would be on the 1000th anniversary of the protectorate! I bet almost every single member in the galaxy should be here right now! I know one thing, right after I graduate I'm going right to the celebrations. Something special is bound to happen!" With this, the problem is solved! And, as for why more didn't escape, and how in the world the evil lady was able to escape, this could be the reason why:
- you could escape because you did it RIGHT when it attacked. As one of the only survivors of the graduation, you could get to a ship that was docked right outside. Most everyone else wasn't as close to a ship, and Earth's destruction happened so incredibly fast that they all died before they could get to one. For those that could, though, they are those that have been "scattered across the stars" as someone in the outpost (A fellow escapee from Earth, i would think) should explain.
- the reason why Bad Girl could get away is because she was holding the crystal. The Ruin didn't see fit to kill her, since she liberated it, so it used its teleporting skills to teleport her right to it, where they proceeded to have a chat about how she would free it. Have it so right after you defeat the ruin, the other "exit" from the room opens, and you can go through it. There is a chest, which has only Bad Girl's journal in it, explaining her side of all this. Have S.A.I.L. say after you continue "Is there not a way out?" (Since there is no teleporter) Then have the Ruin explode. Also, Have The Ruin be sentient. Right After you kill the Bad Girl at the End, The Ruin should have a little dialogue to show this. Something to the effect: "YOU HAVE KILLED THE LIBERATOR, BUT IT'S WORK IS FINISHED. I WILL NOT BE BANISHED AGAIN! DIE WITH YOUR GALAXY!" You can even have the ground rumble during this for effect!

Next, the Eruchius Mining Facility and Eruchius ghosts. PROBLEM, Why did the ghosts only appear after Earth's Destruction? and why wasn't there one at the Mining Facility?

SOLUTION: This one is a little more difficult. If we have the ruin liked to the crystals, and thus the ghost, why didn't it summon a ghost to take care of you? Simple, right? We need to solve that. Being that they should NOT be tied to the ruin, as I just explained, it is a GREAT plot hook for another questline for another race! How? I don't know... Maybe the best solution for now is to simply have it said that the Protectorate knew about these problems with the "ghosts" and that they were linked to the big crystals, and so they made things that would keep the creatures at bay, which were given to fuel miners. However, the power of the repellent things were being pooled from the Ruin Artifact, so when it was removed... poof, no more protection. The crystal in the Mining Facility awoke simply because it wasn't being repressed anymore. That is why this was the first incident as well. How are they going to solve it though? Leaves room for another questline. Whether it be an after the ruin one or a different race's one, idk.

Next, why isn't the ruin destroying other planets?
The solution could be in Bad Girl's journal, as said before. She could have written that the ruin seems to be limited only to the planet that she brought the artifact to, but if she were to open the gate, it would be able to access the whole galaxy once more.

So, These are all the blaring plot holes that I saw, and what I see as some good solutions, but I want to see what everyone else thinks could be done to tidy up the story! I would suggest leaving it mostly intact, since if the developers do ever look at this, they still probably have a good reason (future content) to have the main plot as it is. Don't be "that guy"!

Anyway, I hope to have been a help! (I'll probably add edits if there are awesome solutions and ideas given)
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Just an interesting thought, if alternatively, it was made that while you were taking care of big skeletal dragon robot, she was able to get the artifact, You could go after her, and her confrontation could be that. An effective semi-final boss, with a ton of reveals and awesome stuff like that, and to be able to face the Ruin with a greater knowledge of what is going on. However, that is just a thought.