Nobody knows for sure.
The assumption is that its after the Fate route in which Shirou dies, and meets Saber in Avalon or something.
It's too vague to know exactly how it happened.
"Sion Eltnam is no more.
All there is left is a dead apostle who has inherited the name of TATARI.
Now.....Let's begin the Bloody Second Act." - Sion TATARI