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This guide contains Locations of Crates by Level Please feel free to scrape the guide in order to create a much better one. I am not concerned with credit.
The box with AC parts I discovered was in the “infiltrate grid” quest.

Mission: Infiltrate Grid 08.6

I have not yet found the wrecker arms that I believe should be on this level.

UPDATE. Found the arms—final crate. Also, boxes are visible on scans. However, scans of the head with a good scan are still terrible.

First crate

After you jump into the rafters to take out a single MT drop this hole:

If you kill the other two MTs, turn around to check the back corner of the room you dropped into. Since this area is not on the main path it can’t be skipped. So you should be able find it if you play the level normally while keeping an eye for the spot.

Second Crate

This area is located very close to the 1st crate.

You’ll find a bunch MTs in the ceiling area if you jump across the platform to the left.

Here is the box, BTW they may look different if not collected.

Third Crate

Continue your mission until this Radical entrance is reached… Here’s the screenshot.

Follow the path and you will find some MTs guarding a crate.

Final crate

Bring your guns as you will have a long way to go to find this one. There is an AC guarding it in a tight space. Back to where we got the crate number 2, the platform with the hot metal here:

From the pipe you won’t be able to miss the path.

The missions I’ve found have no crates. They are also so tiny that it seems unlikely I missed any.

Grid 135 Cleaning

Destroy the artillery systems

Destroy helicopters used for transport

Wall climber

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