Updated: See bottom of the page
At the end of season 4 we saw Daniel going off the island in the zodiac, hoping to shuttle people to the freighter. Unfortunately for him the Freighter exploded, the Island disappeared, and Frank and the helicopter people didn’t see Daniel or his group of potential red-shirts.
At the same time Jin was on the deck of the freighter as the bomb was ticking down. He knew he would die if he stayed on the freighter, he missed a ride on the helicopter, and the last we saw of him, he was waving to the helicopter on the deck of The Freighter.
I think placing Daniel in the Ocean going to the Freighter was a way out for Jin. If he jumped off the Freighter Daniel could easily pick him up. I believe that is what happened.
Also I think that Daniel will have some time traveling issues, similar to Desmond in The Constant, due to the island moving too close to him. This will mean that he will need to meet up with Desmond, his constant, in order to stabilize his consciousness.
For more info see the Original Post
Well I was wrong about the specifics, Daniel didn’t save Jin. But I was right in that Jin survived, but anyone could have guessed that.