Martin lost his use of the many Mithias minds aboard, which was a large chunk of the connected minds that made up his network.
But the trade off was more than fair. In his attack BIOPilot had attached himself to each and every one of his victims so he could shut them down.
And as the AI shut down his hosts, Martin left his signature a thousandfold. BIOPilot was riddled with back doors now, and Martin was the key to every one of them.
Martin should no longer be treated as a single entity, he was an infection, that had now spread to BIOPilot.

Martin didn't send him information to process like he did with all the others. Even though the AI would deliver some formidable calculation power, it wasn't the time for being power hungry. The only thing Martin meddled with was the AI's data on himself. BIOPilot would no longer recognize Martin's traces, his marionettes or his codes.

As far as the AI concerned, and his senses had never been off before, Martin and any trace of him had perished in that attack.