Rufus had been disconnected from the machine for quite some time. However, as he was thinking about his strategy to find Marcus, he suddenly felt an overwhelming urge to touch base with the black box which was, for some unknown reason, a source of comfort to him. It helped him to get his thoughts straight. This was the effect of the 'drug' that was implanted in his brain.
This was the machine's opportunity to rebalance Rufus, to try to direct his instincts towards the achievement of a total brain dump of Marcus.
The machine hadn't reckoned on Marcus being dead!