Tomato plants are easy to root cuttings of. I see that your plants are growing in pots there is also a split in the stem which is further limiting the plants uptake of nutrients. When tomato plants get root bound or have a damaged stem, they will often try to root from their stems in search for more soil to be growing in. Add to this desire to root, you have an abundance of moisture which encourages this to occur. From the appearance of the split on the stem, I don't think that the lower main stem can support your plant. The plant knows what it needs to do to survive so go ahead and help it along. I would just cut off the two main stems and plant them in another pot which will allow them to continue to grow roots and perhaps give you a fall crop of tomatoes.
As for your black spots, they appear to be some type of fungus/mold. I will let others comment on that.
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~ Patti ~
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