Reff : This timeline diagram that helps puts things in perspective.
When Barkeep approaches John (who has been living with Jane), they have a discussion while Jane sits on the bench. This is what Barkeep has to say :
And now that you've found her you know who she is. And you understand
who you are. And now maybe you're ready to understand who I am. Now,
listen to me. Listen to me. The shock will wear off but you can take
comfort in knowing that these events are happening in the correct
In the end of the movie they come back to this scene. Where just an additional line is revealed:
You know who she is. And you understand who you are. And now maybe
you're ready to understand who I am.
You see I love her, too.
The Barkeep reveals to John that they are the same person indeed. This is not revealed to the audience however till the end. This is why barkeep says "The shock will wear off".
Barkeep also says:
You're going to save millions of lives. You're about to embark on the
most important job a man has ever had.
Once John knows that Jane, himself and the Barkeep are the same person, he trusts himself (Barkeep) to have made the right decisions and leaves with Barkeep to the future.
With respect to why the Barkeep is doing the things to ensure history is because he is taking inputs from Mr.Robertson, the mystery character. Barkeep knows and trusts Mr.Robertson to make the correct decisions. The Barkeep also feels it is important for him to exist so he can stop the Fizzle bomber, little does he know that he grows old to become the Fizzle Bomber.