How can I get into the giant pit on the second tier?

Walk around to the right side, and you'll see a mantis biot find its way into
the pit.

It activates an elevator by shining a red light at the sensor.

You need to do something similar.

You can assemble your own red light.

You should have a plain light from your locker -- it's one of the options of
the ISA multi-tool.  Press the button on the tool to select the tool's
function.

You also need to make the light red.

You should find something red and somewhat transparent when you explore the
Central Plains.

There's a red crystal shard next to the warehouse.  That's what you need.