The popular NCIS series premiered its episode 5 of season 18 on January 19 and the real reason why Gibbs shot McGee and everything behind this event has been revealed.
In episode 5 of NCIS season 18, we saw Tobias Fornell (Joe Spano), give Gibbs (Mark Harmon) clues that eventually led him to the opioid drug ring they had been investigating.
This led to Nick Torres (Wilmer Valderrama) being nearly killed, and Ellie Bishop (Emily Wickersham) being taken hostage by the mastermind behind the operation: Merriweather. So they had to plan a hostage exchange.
The person who was going to be in charge of the exchange was going to be Fornell, but McGee (Sean Murray) decided to impersonate him, but, in last-minute information, Gibbs is notified that the plane where the exchange would take place had a bomb.
Gibbs came across a sniper rifle from a distant rooftop, but McGee’s communications were down to inform him of the bomb and prevent a tragedy.
So with no way of warning McGee that he was moving towards an explosion, Gibbs decided to shoot his friend until he stopped moving towards the trap and prevent him from dying.