Gibbs mentions his father is dead - but he's saying that to a known terrorist who has just threatened to kill everyone Gibbs loves. Gibbs' response is to show that any target is already dead or he no longer cares if they die (i.e. his ex-wives).
Gibbs mentions that his father has passed on, but his father (played by Ralph Waite) makes his first appearance in season 6 in Heartland (2008).
This was the first time that McGee & Abby both typed on the same keyboard, side by side, to fight off a cyberattack. This is something that they do several times throughout the series.