Hi,

You could possibly have nematodes, in the link there is another link that takes you to a web page with pictures of what it looks like.
Good Luck,
Amy

Here is a link that might be useful: Nematodes

Here is a picture of one of the plant's stems. You can also see the dead leaves on it. There is new growth on both plants, one with a flower.

I got a new tomato plant, should I dig the old ones up before planting the new one?

Here is a link that might be useful: {{gwi:1301169}}

Here is a picture of one of the plant's stems.

That's root primordia, not disease. Nothing to be concerned about.

Looking at what I can see of the rest of the plant, it looks like one of the wilts. If you cut a stem in half, what does the cross section look like?

Also, here's a post on wilts that may be helpful to you in diagnosis if you read through it.

Here is a link that might be useful: tomato problem solver - wilt