Why does the app ask me to reboot after cleanup?

A reboot is needed when malware is running in memory or has locked files that can’t be deleted while Windows is active.

Restarting lets Trojan Killer complete “finish-on-boot” actions—removing leftovers, restoring settings, and unlocking protected items. This is normal and usually takes just one restart; don’t interrupt the process.
If Windows prompts again on the next start, allow the second pass or run a Full scan to verify everything is gone.