The Final Nexus by Gene DeWeese

Uncounted centuries ago, an unknown race from beyond our galaxy built a series of interstellar gates -- shortcuts through the cosmos -- and then disappeared, leaving no clues to their identity nor to the workings of their system. The Enterprise herself has used the gates twice before, without gaining any insight into the mystery. But now the secret of the gates must be solved, because they are disintegrating, cutting distant parts of the galaxy off from each other, and the Enterprise's only hope lies in communicating with creatures from another universe altogether.

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