It was via secure satellite link. They can come to periscope depth, raise the antenna mast, acquire the bird and chat away.
Resupply by ship isn't uncommon either, if it's mission critical especially.
ULF is used for extremely short coded messages, such as come to periscope depth to receive traffic/orders. Voice ain't going that way, as just saying hello would take a week at that baud rate.
I actually did talk to a guy on a sub twice, once for a personal telephone call, once, a case of a sailor doing the "hey, I gotta take a crap, talk with this guy for a bit until I get back". The latter turned out to be a SEAL team member, on a sub going somewhere or something that I had no interest in, made small talk for a bit, then the RTO came back and took over.
It turns out, we chewed a lot of the same sand and were covering each other a few times in mutual aid missions back before I retired. He was thinking of retiring too.
I suggested, "When it starts hurting too much to put all of that crap on, it's time to retire. It's what I did".
Wow, but I still miss my guys!
Nice thing about Army: Nobody comes out of the ground and shoots at you with things that chase you around and won't miss. Navy doesn't have the advantage of being able to hide in a hole while calling in close air. Air doesn't have that advantage either.
Hats off to both!