This guide assumes that you have played through the game, watched the archives, and are familiar with the two other existing Lore guides for this game.

First, let me clarify terms:

• I will refer to the purple-goo aligned beings as "Fungal."
  
• I will refer to the small, single-eyed beings as "Hobs."
  
• I will refer to the cloaked beings as "Cloaks," and
  
• I will refer to the robots as such.

Next, let's the following assumptions:

• The two sentient Fungal beings are not inherently hostile. The Fungal Cloak helps you initially, then attacks if it sees hostile intent. The "Fungal Mother" saves your life (as you know it) before attempting to explain themselves, offering an end to hostilities, and - if attacked - accepting their fate.
  
• The archives, as explained in another guide, refer to a race of sentient beings (likely the Cloaks) leaving an area - let's assume, their home planet - and arriving on a new planet in "Arrival."

If you're comfortable with the assumptions made above, then the conflict this game depicts may not actually be a straightforward case of "good and evil." It might be, but it might not.

My interpretation of the Fungal Mother's monologue is that the Fungal race arrived on this planet, were attacked by the Cloaks who had arrived previously, and retaliated.

The Fungal race prevailed in the conflict against the Cloaks and their robots, as we can see. But strangely, they seem to assist you in bringing about their own demise. Why?

When you enter the world, much of it is below the mist. The reservior is shut off and stowed away, the primary reactor is shut down, and the tower in the middle of the map - well, it's not so much a tower anymore, as a floating island.

As the archives tell us, there is besiegement in the war between the Fungus and the Cloaks. But who is besieging whom?

The Cloaks are simply asleep, and can presumably remain so for as long as is required. You are not awakened by a cloak - you are awaked by a robot. A robot who serves whose agenda?

Not the Cloaks', but the Hobs'.

The robot's innards now function not because of its own power core, but because of the flower in its place. The Hob Mother, who you eventually meet personally, gives you the final power core to the disabled titan - it knows exactly what the titan is going to do, and given how the Hobs have celebrated your destruction of the other Fungal territories, its aim is the assassination of the Fungal Mother.

So, that's the Hobs' agenda - they want the Fungal Mother dead, and all fungus exterminated. But then why doesn't the Fungal Mother want you dead when they see you?

It's possible that the Fungal Mother doesn't actually bear this planet, or its inhabitants, any ill will. The Fungus, like the Cloaks, fled from a planet that they could no longer inhabit. Because they exploited it to the point of uninhabitability? Maybe. Judging by the area surrounding the reactor - a stormy desert with little life - the Cloaks may have done their fair share of this as well.

The Fungal Mother may be fond of the Rogue Butterflies because they, unlike the Hobs, are capable of co-existing with the Fungus. In particular, they seem fond of the yellow surfaces of the Fungus. Of course, you just use them as crafting ingredients for your equipment.

Speaking of that yellow material - what is it, exactly? Judging from the Fungal beings we see with it, the yellow seems correlated with sentience. Could it be that the butterfly roosts you encountered are the remains of sentient fungal beings who were destroyed? Possibly. They do tend to appear after you kill the defenseless blue-eyed fungal creatures. They, like the sword shrines of fallen Cloaks you encounter, may denote lives lost in the war.

Every time you "win" in this game, it is through an act of aggression against a being that cannot or does not directly retaliate. You were brought in to end a stalemate between two factions that cannot co-exist. Cloaks and Hobs is fine, Cloaks and Fungus is fine, but the Hobs want the Fungus dead.

If you join the Fungus, more yellow material appears - possibly because your actions have undone much of the lockdown, and the land has been made more fertile for the Fungus. But the robots will continue the war, either at the behest of the Hob Mother or the long-dead Cloak leaders, and awaken another Cloak. But its possible that Cloak will join the Fungus too, and so on until the Hob Mother has no more Cloaks for the robots to fetch.

If you destroy the Fungus, the robots restore the land to what it once was, and the other Cloaks re-awaken. The Fungal Mother seems to realize this will happen. She sees the situation for what it is, and accepts it.

I'm not saying the Hobs are evil, or that the Cloaks or bad. But it seems to me that the Fungus was just trying to survive. They, like the Cloaks (or perhaps the Hobs?) are alien to this world. Some of its inhabitants welcomed them, others didn't. The spear-wielding creatures certainly don't seem to be fans of the Cloaks, and they may well be natives to this planet, too.

What the Fungal Mother does is, she saves your life, and then places the decision for whether the Fungus will thrive or die in your hands. You are a Cloak. Your kind aren't native to this planet either, but you seem to have made peace with it - more or less. As such, she enables you to judge whether this planet has a place for the Fungus, as well, or whether it shall destroy them. She takes great pains to remove any influence of the Fungus on your mind before you make this decision.

The tagline of this game is, "Make it Home." You will make this planet the home of one of two factions. Your role is simply to pick which faction it will be.

Thanks for reading. If you're hungry for more lore, Runic Games actually posted a short comic to their website that acts as a story prequel to the game. You can find it here:

https://www.runicgames.com/hob/comic/