Lower stem damage like that is unfortunately a hallmark of Southern Blight, which is a fungal disease. The fact that your lower leaves are starting to fail is consistent with that. If that's the case, it's a goner. In the field, if seen on a plant, the way you save your crop is to quickly get rid of that plant. Now, this plant appears to be in a container, and if you used commercial potting mix, such a fungal infection would be very unlikely because those mixes are usually sterile.

It is in a container with commercial potting mix and I used boiling water to pre-moisten it when I initially planted and transplanted, so it seems less likely, but not impossible. The failing leaves are the seed leaves. They have been like that for a couple weeks now - I think they have just finished their job.

The bottom leaves on the far right of the bottom picture aren't seed leaves, and they look very yellow. Boiling water will disinfect the top layer of soil. Not further down. But yes, commercial potting mix is unlikely to harbor such a fungus.