| Season 3|
- Franks first appears in 3.23 Hiatus (Part I) and 3.24 Hiatus (Part II). He is introduced through a series of flashbacks. Franks was the NIS agent at Camp Pendleton investigating Kelly and Shannon's death. Gibbs came to ask him questions and that he legally was unable to answer. He "left" the room, leaving the sniper file on the desk. This ability to bend the rules when he feels it best serves justice is a trait he obviously shares with Gibbs.
- Gibbs joined NIS because of Franks. Per tradition, Franks called him 'Probie' then and still does to this day. According to Franks "I investigated crime scenes. You schlepped." He even tells Gibbs "Never say you're sorry. It's a sign of weakness." Franks retired to Mexico in 1996 after his warnings about the Khobar Towers were ignored. He has since cut himself off from "El Norte," building himself a place on a beach in Baja. "No TV, no radio, no newspapers. I fish. I drink beer. Listen to old eight track tapes. Drive to a cantina up the coast when I want company… when the pickup’s running."
- Jenny calls him in 3.23 Hiatus (Part I), asking him to return in the hopes of jogging Gibbs memory. Mike is shocked to find that NCIS is now run by a woman.
| Season 4|
- It is to Franks that Gibbs goes when he retires. He has been staying with Franks 4 months by the time Ziva calls in 4.01 Shalom. Gibbs has been trying to fix the roof since hurricane season is coming and the house is rotting around them. Franks wants him to lay off, relax, and perhaps build a hot tub.
- The case the team is working in 4.04 Faking It involves an old case of Franks. He is called back to help the investigation and catch the man who had eluded him before. He comes because “These scumbags have been selling weapons to tyrants and terrorists ever since they gave us the slip … It’s time it ended.” He gives Tony the slip and goes out on his own, bending the rules again to take down the criminal.
- In 4.18 Iceman we find out that Franks has a son which he's only known about for about 2 years. The son was smuggling his Iraqi fiancée and infant daughter to America when things went wrong and he is left in a coma. Franks risks everything to finish what his son started and to catch his son's killer. His behavior tests his relationship with Gibbs, but Gibbs understands what family means and helps.
| Season 5|
- Jenny called Franks to help her in 5.18 Judgment Day. He was uncertain to help at first but when he found out Gibbs was involved he immediately said he'd help. At the diner, Franks went outside to get water, but when he did the 4 gunmen came in to kill Jenny. Franks fired a few times then later came in and shot the gunmen to make sure they were dead. He "did what he could."
| Season 6:|
- In 6.15 Deliverance, Franks comes back when Gibbs sees his service number in blood and he knew that Rose, the woman that Mike brought from Colombia in 1991, knew that number, but she is dead and Mike did not tell Gibbs that Rose had a son, who was a year old when Mike brought her to the states, knew his number from Rose and Mike helps during the investigation.
| Season 7|
- In 7.06 Outlaws and Inlaws, Franks shows up at Gibbs's home with Leyla and Amira and tells him to find out who is after him. Investigation reveals that the actions have been prompted by Leyla's mother, Shada. Franks and Shada eventually reconcile for the benefit of their mutual granddaughter.
- In episode 7.24 Rule Fifty-One, Franks has a gun-battle with the men hired by Colonel Merton Bell. Franks was injured in the battle (losing the end of his trigger finger), but is still is alive and claims that he can still pull the trigger with his thumb. At the end of the episode, Franks finds DiNozzo shadowing Alejandro Rivera and assumes that duty himself.
| Season 8|
- In 8.23 Swan Song, Mike Franks is killed by Jonas Cobb (the "Port to Port Killer") while fighting him to protect Gibbs. Franks already knew that he was near death from lung cancer but claimed to have "one last fight in him". Franks left Gibbs with the box of secret files amassed by Franks' own NIS boss, William Dekker, in the hopes the files could be useful to Gibbs sometime in the future.
| Season 9|
- In 9.14 Life Before His Eyes, Mike Franks' spirit returns to help Gibbs understand the (mostly positive) consequences of Gibbs' decisions throughout his adult life. Although Gibbs has interactions with several other spirits, it is Franks that puts those conversations into perspective.
| Season 10|
- In episode 10.24 Damned If You Do, Mike Franks' spirit returns once more to serve as Gibbs' conscience, finally inspiring Gibbs to fight back against the accusations laid by Investigator Richard Parsons.
| Season 11|
- Episode 11.04 Anonymous Was A Woman also features Mike Franks in a series of memory flashbacks. It is revealed that during the last few years of his life, Franks had helped smuggle oppressed women out of Afghanistan to start new lives in the United States or other countries. At one point near the end, he had asked Gibbs to help by transmitting orders authorizing military transport for six women, but Gibbs refused to break the law on this point -- he was unable to condone human trafficking. Gibbs eventually follows Franks' lead and transports several endangered women to the US.