SPOILER ALERT: This story contains details about tonight’s season finale of CBSNCIS.

“Were you and Ziva an item the whole time?” asked NCIS Special Agent Timothy McGee (Sean Murray), to Michael Weatherly’s Special Agent Tony DiNozzo. “We had a…connection,” answered DiNozzo, “and obviously a very fond farewell.”

Obviously indeed. Tonight’s big surprise on the Season 13 finale of CBS’ flagship drama series: Tony and Ziva — whose relationship was always more suggested than demonstrated — have a daughter, an adorable little girl named Tali (played by twins Emelia Golfieri and Layla Golfieri) who was hand-delivered tonight by Israeli officials to DiNozzo, following the apparent death by explosion of Ziva.

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Suddenly, Weatherly’s hints last week that his final NCIS episode would seem “Shakespearean” made some sense. “DiNozzo loses a love, gains a child,” said Laura San Gicacoma’s psychiatrist character Dr. Grace Confalone, making a guest appearance.

The unexpected twist not only gave de Pablo’s Ziva a sort of spiritual presence in what was the final episode of original cast member Weatherly (de Pablo was shown in flashbacks throughout the episode, in keeping with the actress’ recent disclosure that she wouldn’t be returning for new scenes). But it also gave new dad DiNozzo a credible reason for leaving his job as NCIS’s perennial No. 2.

“I’m everything to that little girl now,” DiNozzo told boss Leroy Gibbs (Mark Harmon), just before resigning his job to take little Tali to Israel (for answers) and then maybe Paris (for fun).

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And so Weatherly ended an emotional episode without his trademark smirks or wisecracks, handing in a tear-soaked season finale that finally confirmed DiNozzo’s relationship with Ziva went beyond a tarmac kiss a few seasons back. The finale also saw a return by Robert Wagner, who has recurred as DiNozzo’s dad, this time around encouraging his son to take some time for an emotional breather.

The episode not only brought an end to Weatherly’s tenure, but closed the door on one of the show’s more intriguing running storylines: the multi-episode arc about the serial killings of NCIS agents past and present. At first assumed to be the deadly doings of a rogue British MI6 agent, NCIS revealed last week that the Brit had been set up by Trent Kort (David Dayan Fisher), the one-eyed former CIA operative and nuclear secrets spiller who’s been as close as NCIS has gotten to a Dr. Evil over the years.

The gun-toting Kort met a particularly violent end, by NCIS standards, as the entire NCIS gang opened fire on him. DiNozzo, of course, got off the first round.

And with that case wrapped up, the farewells began. “I know how much Ziva really loved you,” the ever-goth forensics expert Abby Sciuto (Pauley Perrette) told DiNozzo in a tearful goodbye. “I know. She told me.”

DiNozzo had hug fests with McGee and agent Ellie Bishop (Emily Wickersham), and Harmon’s Gibbs, of course, before heading home to the little girl he never knew. Weatherly’s final episode, written by Gary Glasberg & Scott Williams and directed by Tony Wharmby, was titled, appropriately enough, “Family First.”

As for Weatherly, he’ll be returning to CBS even if his character isn’t: The network has given a series order for Bull, in which Weatherly plays a jury consultant inspired by the early career of “Dr. Phil” McGraw. Weatherly is expected to appear at CBS’ upfront presentation in New York tomorrow.