This debate flows primarily from a difference of opinion regarding what the word 'morality' should be taken to mean. Predictably enough, the atheist believes that morality is an instrumental package of norms useful for humans to get along and thrive on Earth, while the theist believes that morality is a set of transcendent truths which exist in a supernatural realm accessible to us only by mystical experience or divine revelation. They each make their respective cases reasonably well, but for the most part they are talking past each other about different ideas.
Both speakers are notably jolly and upbeat, which is a nice change of pace. Possibly this is the most friendly debate I've seen since the one at UCO back in 2003. I'm sure that I've never heard someone accuse atheism of the 20th century genocides in such a friendly and deferential manner as Fr. Jacobse.
On a side note, the video production values on this are through the roof for a student-produced YouTube video, which bumps my rating up just a bit.