Malachi had been Consul for more or less sixteen years. He lived through the Uprising and, when the Inquisitor died in the battle, he named Imogen Herondale as the replacement. His logic was that no one would hunt down the Circle members more fiercely than she would. He went on to live the next sixteen years of his life in Idris, advising the Clave as the Consul.
When Inquisitor Herondale died, Malachi was given the job of naming her replacement, and he chose Aldertree. He advised the Council against letting the Daylighter Simon Lewis leave Alicante, saying he had broken laws and should be punished. He was overruled and agreed to allow Simon to leave. However, he and Aldertree secretly planned to imprison and interrogate Simon to have him put the blame on the Lightwoods for the attack on Valentine's ship. When Alec Lightwood brought Simon to the Gard, he made no effort to hide his disdain for Simon and gladly escorted Alec out when Aldertree asked him to.
After the invasion of Alicante, Malachi got into an argument with Luke Garroway. He tried to blame the werewolves for the attack, though they had in fact helped in the ensuing battle. When Luke said that the Clave would need the help of Downworlders, Malachi denied it, saying that they could fight their own battles.
Malachi was present when Valentine came to tell the Clave of the upcoming attack on Brocelind Plain. He tried to hold back Aldertree from attacking Valentine; he failed, however, and Aldertree was killed.
Later, he noticed Clary spying on him after meeting with Valentine. He argued with her over the moral rightness of what Valentine was planning. He was fearful that Valentine would turn all of the current Marked Shadowhunters, including him, into Forsaken as collateral damage for his plans when Valentine summons the angel Raziel. After Malachi knocked out Valentine's raven Hugin, the raven subsequently attacked him. Malachi fell onto broken glasses on the floor and died when a jagged shard pierced his throat.
- City of Glass (first and only appearance)