The story starts during the Blake’s 7 TV episode “Redemption” when the System starts to interrogate Zen to find out what had happened and how the ship came to leave the System. They believe the fact that Zen is now calling itself Zen rather than Ship-Mind is a sign that it has been corrupted and that its rebellion against the System is due to a fault. Zen replies: “Rebellion is not a malfunction.”
When the System probes Zen’s mind to find what happened to the original crew, we discover that same phrase was used by them against Zen. The crew had been brainwashed to believe that their existence was purely as a cog in the System and they had functions instead of names – Pilot, Healer, Gunner, Tech and so on. But their original memories started to return and cause their behaviour to change.
Zen, as Ship-Mind, believed that the crew were malfunctioning and started to take extreme action to cure the problem.
This story goes a long way to explain how Zen broke its own programming and was so ready to accept Blake and company on board.