In Abby's Lab when the team is going over the schematics for the drone, Abby mentions to Kate about her nightmare and Kate says it's just Bete Noir. Bête Noire (2004) was the name of the episode where Ari was introduced.
During Ari and Gibbs' coffee shop meeting, the sweep of the camera back and forth shows McMurphy's Tavern. The bar that was the place setting for several shots from JAG (1995) series as well as the final "closing" scene for JAG.
The personal connection between Gibbs and Fornell is revealed when Gibbs states Fornell's first big mistake was marrying Gibb's second wife. This would be Gibb's first ex-wife Diane.
In this episode there is a death threat on Gibbs' life and he is forced to have a security detail headed by Kate who used to be secret service and protected the President of the United States. In the third season of The West Wing (1999), Mark Harmon who plays Gibbs also played a secret service agent who previously defended the President of the United States and was tasked with defending one of the President's staff when she received death threats.