He used the team computers foolishly. He’d been doing internet searches on creating a fake identity, escaping from cults, etc. for several months, tipping off the elders that he was planning to escape. His big mistake was purchasing a bus ticket to Texas, from where he was planning to run for the border.
The strike team apprehended him on his way to the bus station, killed him before he knew what was happening, and disposed of the body in a way that guaranteed nobody would ever stumble upon it.
One of my favorite parts of writing Mercury is playing with Deep POV to show subtle differences between him and Jill. For example, Jillian is always honest if she was crying. Benjamin, on the other hand, comes up with a bunch of different euphemisms for his tears.