In December 2007, when the Clave called for Shadowhunters around the world to evacuate the Institutes and retreat to Alicante in light of Sebastian Morgenstern's attacks, Tomas was convinced that Idris would not be safe and insisted that Cristina and her mother stay in hiding in their house in Mexico.
Once at Alicante, Tomas was among the Institute heads who spoke out during the Clave and Council meetings in Alicante in preparation for the war against Sebastian. Tomas then participated in the Citadel battle against Sebastian's Endarkened warriors, during which he sustained an injury on his arm that was later bandaged up.
When the Council found out that there was no way to bring the Endarkened back, they also realized that the only way to deal with them was to kill them; Tomas, however, was horrified at the thought of killing all the Endarkened "in one sweep" through the destruction of the Infernal Cup as he still saw them as fellow Shadowhunters. When they were told that the faeries were in league with Sebastian, he became concerned and, in frustration, called the former Silent Brother Zachariah, who was advising them about the Endarkened, a boy.
Tomas was among the casualties of the war.
- City of Heavenly Fire (first appearance)
- Lady Midnight (mentioned only)
- Queen of Air and Darkness (mentioned only)
- It was Cristina's father who was initially meant to be introduced in City of Heavenly Fire as the head of the Mexico Institute.