- "Academy to Yavin Runner II, do you copy?"
- ―Luke Skywalker contacting the ship
In 14 ABY, while bringing a group of new students to the Praxeum from Coruscant, the Yavin Runner II was shot down by Tavion Axmis as a diversion. It crashed several kilometers west of a Massassi Temple. The students were unharmed but had to be picked up by a shuttle. In the meantime, Alora, one of Tavion's cultists infiltrated the Academy and sliced into Luke's records.
A shuttle similar to the Yavin Runner II was later flown by Jaden Korr on a rescue mission to Blenjeel. The ship crashed in an electric storm but Korr was able to repair it with parts from the ship he came to rescue.
- Star Wars: Jedi Knight: Jedi Academy (First appearance)