Spoilers ahead for Episode 4 of Legends of Tomorrow Season 3, called "Phone Home."
Legends of Tomorrow went full E.T. in "Phone Home" as the Legends went back to Ray's childhood in 1988 to prevent him from being killed by government men after he took in an alien. The whole episode was full of 80s fun and references to all things E.T., but the hour wasn't just about saving young Ray's life. In a side plot, Mick and Jax began to suspect that Stein was up to no good after they discovered he had built a communicator that worked throughout time and he had taken the jump ship out for a secret mission. While at first they thought that he was a spy for Rip's new group of time police, he eventually came clean and admitted a secret that is probably going to take him out of the Waverider for good: he was visiting his daughter.
The show revealed earlier this season that Stein's adult daughter (who didn't exist prior to Season 2) was pregnant and expecting to give birth in the not-too-distant future. Although Stein was clearly excited at the prospect of becoming a grandfather, he nevertheless returned to the Legends team on the Waverider. Now it seems that Stein wants to prioritize his family back in 2017 over bumbling through missions with the other time travelers. Given that we learned not so long ago that Stein would indeed be departing due to actor Victor Garber's new role on Broadway, it's probably safe to say that this is why Stein will be leaving the Waverider behind.
A big question that arose out of the news of Victor Garber's looming departure was how exactly Legends of Tomorrow would handle Firestorm. The two halves of Firestorm need each other to survive, and it seemed like the show would need to write Jax out of the show at the same time as Garber, kill off Stein and find a new half of Firestorm for Jax, or simply have Jax and Stein meeting off-screen on a regular basis as a way to keep Jax on board without Victor Garber to play his other half. In "Phone Home," Jax decided that he wanted Stein to have the chance to be with his family and asked Ray to help him figure out a way to split Firestorm.
If Ray and Jax are successful in finding a way to split Firestorm, Legends of Tomorrow would be able to keep Firestorm as a hero, write off Victor Garber without needing to get rid of Jax, and not kill anybody off. That's not to say that Stein is totally free and clear from being killed off, but I'd say his odds of survival are pretty great at this point. We probably won't have to wait too long to see.