Apple tree is toast

I have one of my bare root apple trees that just did not do well from the start and after pulling it out this is what I found, any ideas? What should I do to protect the others that are nearby?

Don’t pull them out!!!

Sorry I couldn’t help myself. But seriously the small roots look good. I’m not sure if the black stuff is a issue.

I was actually more concerned about it being all knotted up. Also the bark on the graft was pulling away and when I cut off the top it was turning brown under the bark

The knots on the root could just be root knots. They are talked about when above ground but not when below.

Now bark pulled away and brown under bark, both obviously bad. Sorry I can’t help on that. Could be fire blight or crown rot. The upper part of tree, bottom of picture, looks OK.

I could be completely off base here but it looks as if he tree may have been planted too deeply. If so the burr knots may have tried to develop roots after the knots were formed. Planting too deeply has caused more than one tree to die in the history of man.

TCT, 4 inches above graft same as all other trees.