(Original Timeline) In the Pentagon, John F. Kennedy, Richard Nixon, and Robert McNamara meet with Fidel Castro in the aftermath of the Cuban Missile Crisis. Due to the vents at the cosmodrome, a zombie outbreak occurs. Samantha sends Yuri to the Pentagon to thwart their survival. After Gersh is freed and Ultimis departs from the Cosmodrome, the outbreak ends at the Pentagon. All four survive. It is unknown what happened to the crew afterwards.
(Agonia Fracture) Hiding in a closet at the Pentagon, McNamara records a message confirming that John F. Kennedy, Richard Nixon, and Fidel Castro have died as a result of a zombie outbreak. He dies moments later.
Kennedy appears in a small Easter Egg in Ascension: He can be heard through one of the three red telephones, which start to ring after certain events in Ascension. He says one of his "out-of-ammo" quotes - "Need some beans for the chowder here!" along with the other members of the crew, except for McNamara, who was hiding in a closet.
Unlike most of Zombies playable characters, Kennedy doesn't have any quotes after being downed by zombies.
When using the Winter's Howl, he can sometimes say, 'Ice ice baby', which is a reference to the song of the same name by Vanilla Ice.