One plot idea could be that Malcolm Reed contracts a disease that slowly drains his life force. As he gets sicker, he starts to have visions of his past and future. These visions could be used as a device to explore his character more deeply. His crewmates, especially Captain Archer, are determined to save him. They visit various alien races in search of a cure, and along the way, Malcolm's relationship with each of his friends is tested and strengthened as they all face the possibility of losing him.
A simple plot could be that Malcolm gets sick due to a contaminated food source on a newly discovered planet. The crew has to quarantine him while they search for a remedy.