This one is a sort of an elegy, though not to anyone specific. It tells a sort of mini story as well. The first verse is a young man attending his deceased friend's funeral. In this first verse, he is experiencing the natural pain and sorrow gained by losing someone you truly care about.
The pre-chorus is basically him beginning to realize the positive side of it all. The third line of the pre-chorus is meant to sung by a female, as well as the chorus.
The chorus is his friend up in heaven speaking to him in his heart, not that this can be done. Its merely him realizing that she is in a better place now. When it says "We're sure to meet again soon", it's talking about how all human life is short lived. We don't spend very much time on this earth at all. And, the end times are also approaching inevitably as the scriptures say. So, if it is looked at with this perspective, it will be more easily understood.
The second verse talks about the man reflecting back to the good times they had together. Since this is merely a song, not a book, I am not able to describe the whole story in one song. When he says that he neglected their friendship, he is reflecting to their recent argument which broke up their friendship. His friend had died in an unexpected accident a day after they had stopped being friends. He wishes that they could have had more time together and he regrets even fighting in the first place.
In the bridge, it talks about him wishing he could have apologized to his friend before she left this world. But he then realizes that she is in a truly better place now. A place where there is no pain, sorrow, or death. A home where will love will never cease to exist.