so far i think that the timeline order is: 2D-3D-milkman. though i have another theorie, which i will keep a secret because i am not sure about it.
in his teens\young adulthood our protagonist is going wild on the city buildings. he kills a lot of "badguy's" as he names them. (end 2D) but on a certain day he is captured and imprisoned. he escapes from captivity and, somehow, finds his way to the sky. (end 3D, tutorial and sandbox i don't consider canon) when he is older he needs to go to the store, the people who captured him are back and try to kill him! (end Milkman)
if you have your own theorie, leave a comment