A mysterious contract

We arrived at the pick-up coordinates and we're currently waiting the transport ship. For once, we didn't encounter any Raptures, i take a rest enjoying the moment while Rapi and Anis look for any intruder while staying in a position that allow them to rest. I sense their eyes on me wanting to ask many questions about me however they stay quiet about it.

Finally, the transport ship arrives and we all get in.  The trip was very quiet until we've landed in a sort of hangar. Then a hidden elevator appears and now we are all going down to the Ark. Marian was still sleeping and snoring gently on my left shoulder, it was very cute. This moment could be passing in silence however Anis decides to speak up.

Anis : Shifty. Marian. What's going on?

Shifty : That corrruption code implanted into Marian's brain must be acting as a navigator! It guides Nikkes to the Blacksmith's location. That way, they're having their 'food' delivered straight to their doorstep.

Anis : But she was acting completely normal before she went haywire.

Shifty : That's probably because of the Commander.

Lowell : Me? Why am I probably the cause?

Shifty : Because a Nikke's highest priority is protecting their Commander and obeying any orders given. I'm willing to bet the problem started when she met the Commander. That's when her priorities were shifted out of order. She was completely defenseless when in close proximity to the Blacksmith. That means the corruption was quite severe.

I was utterly confused. How can a brain become corrupted? She was only hit with bullets from Raptures. I don't think it's somethink that can be done remotely because Anis and Rapi aren't corrupted. I need answers about this.

Shifty : But when I've managed to recontact you, Marian was no corrupted. Commander, Anis, Rapi, can you tell me what happen while I was gone?

Lowell : ...

Anis : ...

Rapi : ... The corruption have removed itself on Marian.

Shifty : What?! How?!

Rapi : When we've defeated Blacksmith. We found Marian near his body. I went to her to check her state and I remarked that i didn't detect any corruption from her, it's like it was magically gone.

Shifty : ...

Rapi : ... When did it start?

Shifty : What?

Rapi : When was she first corrupted?

Nice save Rapi!

Shifty : During the operation, I suppose... Ah, yes.

Rapi : You said she was the one that sabotaged the transport ship, right? She must have already been corrupted at that point. And that transport ship came from the Ark.

Shifty : !! Were the Aegis Barriers broken?

Rapi : No, the Aegis Barriers are strong. They'd pick up any corruption in an instant.

Anis : ... Rapi, what are you trying to say?

Rapi : Well...

I know what Rapi will say next, it was the only logical theory but with only guess we cannot confirm this. So I stay silent and away from their dicussion.

The elevator keeps descending and I saw the Ark. Numerous lights illuminated this city in a cavern. I look around to see other elevators converging to the Ark. I must admit it was a pleasant susprise. I thought the Ark was a boring grey color and overwhelmed with despair however with this much glow from the Ark. I take a few photos with my phone for my report.