A lot of people say the whale and the astronaut/space concept did not make sense in the Sing For You MV, but it actually has a lot of significance.
The whale concept was derived from the a whale called Alice aka ‘The Loneliest Whale in the World’, who is an unidentified whale species, being the only whale emitting a call at 52-hertz.
The astronaut concept was derived from the story of the astronaut who spent 48 minutes in his spaceship and coming back saying that those 48 minutes were the longest and most loneliest of mankind.
The combination of these two concepts placed within the MV discusses being away from home, being somewhere unfamiliar (since the whale and astronaut is in space) and being isolated. Isolation was one of the themes in the mv (when Kai was seen being alone when the other members were playing/when Chanyeol and Suho were fighting).
The song and the MV seems to talk about how everyone, in their lifetime, would meet a low point where they feel most isolated and most out of their place, but that this song (and EXO) will be there to warm their hearts.
In a way, this song could also be indirectly dedicated to the members who have left considering the lyrics of the song.