novel - Story: space colonization with sentient/telepathic spaceships, also genocide and reincarnation

When I was younger I visited my local library quite frequently. I loved picking random fantasy and sci-fi books and reading them. There is this one book that I read and it seemed to be part of a bigger series. I can't remember the name at all. It was more than a decade ago.

The story takes place in the future. Humans have colonized many new worlds. The author writes from the perspective of many characters. Good ones and bad ones. The most interesting part of the book were the people that returned from the dead. They were not zombies or anything like that. They returned from some kind of darkness. I don't know if you can call it hell. The people that returned took over the bodies that belonged to living people. I don't remember how they did it or when it happened. They also got some powers if I recall correctly.

What else do I remember? Hmm, the space ships were alive and had some kind of connection to their captains. There was this one female soldier that had a brain implant. She was able to load some zero gravity close quarter combat skills into her brain to kick somebody's ass. I think there was also a huge genocide, where a whole planet got wiped out.

I hope this is enough for some people to recognize the book I am talking about.

Answer

Thanks to Moriarty, I found the book I was looking for. It is called The Neutronium Alchemist and is the second book in the Night's Dawn Trilogy.

Link to Wikipedia

The Neutronium Alchemist is a science fiction novel by Peter F. Hamilton and is the second book in The Night's Dawn Trilogy. It follows on from The Reality Dysfunction and precedes The Naked God.

Here are some snippets from the plot summary, which contain a few things mentioned in the question:

[...] On Avon the Confederation Assembly is stunned to learn of the threat from the possessed. [...] The Kiint ambassador reveals that, many thousands of years ago, they also suffered a 'possession crisis', as the secret of death is one that is eventually discovered by all sentient races. They claim that their solution to the crisis is not applicable to humanity, who must find their own way.

Alkad Mzu departs from the blackhawk Udat, leaving behind a virus in its jump system which causes the destruction of Udat whilst making a wormhole transit. She does this both to protect knowledge of her whereabouts and also as revenge: Udat was one of the blackhawks which crippled the Beezling just before the Garissan Genocide.

[...] On New California a few possessed manage to get loose on the planet, but they are disorganised and unable to make much headway. One of the possessed appears to be a raving lunatic, but as the days pass the possessing soul's presence in a normally-functioning brain restore his sanity and his memory. The possessing soul turns out to be Al Capone, a famed gangster from 20th century Chicago. Capone organises the possessed and they take over the planet in a matter of weeks. Capone realises they need to keep the planet's economy and starship-building capability going to defend themselves from any counter-attack, so many citizens are spared from possession (the act of which interferes with electrical systems nearby) as long as they contribute to the expansion of Capone's 'Organisation'.[...]

This is from the "The Reality Disfunction" wikipage:

[...] but not before one of the possessed reveals a terrible secret: the possessing entities are the souls of humans who have died and been trapped, some of them for millennia, in an absolute void where the only way to pass the time is to parasitically feed on the memories and experiences of others. And there are billions of them in the darkness still screaming for escape.

I remember how the possessed feared to go back into that void. They are able to withstand all kind of torture when people try to force them to go back. The only way to free someone is to put them into stasis and wait for the possessed to leave, iirc.