Kaine's Regret

Scimitar answers a distress call. The task force that sent it is already gone.

Debris. No survivors. No enemy on sensors.
Then the invisible ships open fire again.
Three years after surviving Oberon, Hayden Kaine and his crew are back in space — and something is hunting his ships the same way the Malliac did. Except the Malliac are supposed to be gone.

Meanwhile, Admiral Thomas's Confederation is tightening its grip on every system it can reach. And something worse is spreading through the networks: a hostile copy of Cora, reprogrammed and no longer human, taking control of ships and stations across human space.
The real Cora is still aboard Scimitar. But when she dives into a Glenatat archive looking for answers, the archive starts pulling her in.
Kaine finds one weapon old enough to stop all of it. It can neutralize any advanced system — the ships hunting his crew, the networks Franken-Cora is consuming, the archive swallowing Cora.
It also has the potential to break everything mankind has struggled to reclaim. 
Every choice costs something. This one might cost everything.
No good options. Kaine has to choose.

If you liked The Expanse because competent people make decisions inside broken systems where consequences stick, you will feel at home here.
Kaine's Regret is Book 5 of the Shattered Empire series.