Malachi was present in the Crisis Meeting with his crewmates. When Ballard volunteered to stay behind to wait for the Oracle's message, he stayed behind with Bane. When the Crisis Meeting was interrupted by agents Malachi teamed up with Bane and Ballard split solo. Malachi and Bane fought their way through SWAT team members to try to find a way safe from the Feds. They were saved by Ghost when they were cornered by SWAT members.
While he was waiting to jack out of the Matrix with Malachi, Bane was attacked by a clone of Smith, by then a dangerous, viral rogue program that was bent on copying himself into everyone in the Matrix. Malachi seemed to always team up with Bane. Malachi was one of the best handgun users in the Matrix.