During season 18, episode 5 (titled “Head of the Snake”), it's revealed Gibbs shot McGee because he was trying to protect him from getting hurt. There was a bomb on the plane, and McGee was running straight toward it. If he had gotten any closer, he would have been blown to bits.

Does McGee shoot Gibbs?

No, your eyes weren't deceiving you in the opener of the NCIS Season 18 premiere: Gibbs (Mark Harmon) really does shoot his agent and close friend McGee (Sean Murray) not once but twice as the CBS procedural catches up to March 2020 (its present-day).

Did NCIS kill off McGee?

NCIS teased a pretty huge event in the Season 18 premiere with a flash-forward, in which Leroy Jethro Gibbs gunned down Timothy McGee with a sniper rifle.