In December 2007, during the Dark War, the Basilias was once again used after the battle at the Adamant Citadel, accommodating Shadowhunters injured in the battle with the Endarkened. Jace Herondale and Brother Zachariah were taken there after Jace was stabbed by Sebastian, awakening and releasing a surge of heavenly fire from the wound, affecting Zachariah as well. Jace insisted on leaving against the Brothers' advice, suspecting that he was being kept there so his heavenly fire could be studied. He met Zachariah, reverted back to his human form due to his heavenly fire, in the Basilias.
The Basilias is a large stone building with steps leading up to double doors. When open, the building is brightly lit by witchlight.
The infirmary hall in the Basilias was a long room that housed several white-sheeted infirmary cots, with arched windows between them. The hall has an arched ceiling painted with interlacing designs of healing runes in silver and blue, and the floor is made of marble. The Basilias also has private rooms. The hall and the rooms can be reached through a common narrow, white-plastered corridor.
- Only Shadowhunters are allowed to enter the Basilias.
- Shadowhunters with psychological problems—referred to only officially as lunacy by other Shadowhunters—are kept confined in the Basilias.