It is unclear how McDonnell died, either he was killed by the Sulyvahn's Beasts, or from the black goo under his eyes, he may have been exposed to the Deep itself.

What happened to Archdeacon McDonnell?

Archdeacon McDonnell's mummified remains can be found in Irithyll of the Boreal Valley, at the Water Reserve. ... Archdeacon McDonnell's remains are located at the far-left corner of the hall, near the Water Reserve bonfire, which will appear once both beasts have been defeated.

Can you kill Archdeacon McDonnell?

Archdeacon McDonnell Information

Cannot be killed for he is already dead. Covenant Leader for Aldrich Faithful.