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The novel has several story lines going on at the same time.

The one I remember the most is inside a giant spaceship, we are talking many km long. The captain of the ship is kept frozen due to a parasite that spreads when he is unfrozen. The main character seeks his advice from time to time by thawing him a little so his brain is active enough to talk on the machine.

He acquired the parasite when he and another crew member went into a sea of aliens/information. Later on, it was revealed that the captain actually replaced the crew member's mind with his own when they were in the sea. In the end he was thawed and the parasite took over the ship.

Another story line had something to do with ancient alien ruins and advanced aliens hiding behind black holes that would kill off life in the galaxy every once in a while.

28

That's definitely Revelation Space by Alastair Reynolds, which is the first of a series. A couple of names that may ring a bell and confirm it: the captain's infection is called the Melding Plague and the Inhibitors kill off life in the galaxy.

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