Provisional Site-43 is to research SCP-3488-T, and figure out how it managed to evade any form of detection through any means available.
This sentence is pretty sloppy, mostly due to the vagueness of the last phrase. I'd recommend rewriting this.
Underneath the northernmost roots of SCP-3488-T is a roughly circular opening in the ground, and a tunnel running in the direction of the trunk, which leads into a cave approximately 10 meters below the surface
I didn't understand what is happening. Is the circular opening the tunnel? Is it a separate opening?
The distance and direction of this system would place the opening approximately underneath the center of the trunk of SCP-3488-T, however past this opening is a large valley, designated SCP-3488-V, extending approximately 3 kilometers out from the opening in all directions, filled with a forest of SCP-3488 instances.
This is not a good sentence. It's too big and is trying to do too much.
These SCP-3488 instances possess identical markings and "injuries" from being eaten by said reptiles, along with other identifying characteristics. The reptiles also share this quality, with each of them having an identical appearance and location relative to their outside counterparts.
These sentences are not necessary, as the previous sentence explained it already.
Once at SCP-3488-S44, SCP-3488-L gnawed at the growing shoots, seemingly trying to bite them off.
Assuming intent when describing an entity's behavior is generally frowned upon. It is easier to say that it gnawed at the base of the growing shoots.
Overall there's something here, but the idea focuses too much on the details that don't really matter. The language here feels like it is constantly stating something and then elaborating on its previous statement. This is good for clarification purposes for unclear language but what's better is just having clear language.
From a structural standpoint, it seems mostly like a hook with no followthrough. This would be effective if it was maybe half its current size because it would be a quick and mysterious read. Its current length makes it feel like I have slogged through this with nothing to show for it.