Background: Originally, the Sniper had gotten fed up of "...getting picked on by men my own size!" The Sniper had finally reached the last straw when bullied by an enemy Spy. Later the Sniper is looking through a Saxton Hale catalog and finds Jarate. The Sniper then uses the Jarate to get back at the enemy Spy who was teasing him, and the rest is history. I assume this is why Jarate is always associated with Sniper vs. Spy rivalry and was released in the Sniper vs. Spy Team Fortress update.
My Original Theory and what others thought came from before the comic release told us all: Before doing research into Jarate, I assumed that, because the sniper was an outdoors hunter and bush-man, that one day, in the middle of the night while sleeping that he was too lazy to get up and take a pee. Then the Sniper proceeds to pee into the improvised water carrying jar by his side and the next day is in some crazy situation where he is being attacked by some animal/merc and the only thing he can reach for in time is the pee. Of course, you can see how my theory goes on from that.
Note: None of this above is real...Only what I assumed had brought Jarate into the picture.
Jarate in-game qualities:
-20 second recharge time
-Duration 5-10 seconds
-Soaked enemies take mini-crit damage
-Partially nullifies cloak on enemy Spies
-Extinguish flames on yourself and teammates
-Can be deflected with Pyro airblast
Sniper class token + Secondary slot token + scrap metal = possible Jarate
(What I mean by that is that this combo can craft other tf2 items as well)