Well, MK have so many events that the time when they occurred it is really confusing. Can anyone make a time line with all the story line events, since the beggining of the realms when the Gods defeated One Being, until now in Deception. Some non cannon games could be considered, like Special Forces and Shaolin Monks. To me these are non cannon.
I just saw exactly what you are looking for 2 days ago, if I find the link that contains practically the entery story (inclduing MKM and MKSF) I will post it here for you. Its a complete text of all the events of Mk.
BTW, it was Shao Kahn who killed Onaga by poisoning him, not the elder gods.
Here! I just found one. Im NOT sure if its accurate or complete, most of these guides are done by great fans, but some facts can be mistaken. I think Kombat did this one so its safe to assume its a good story guide.
BTW, Zidane, MKSM is (sadly) considered cannon in most of its story. In the fight Night interview Boon and the team talked as if it was. Hopefully some elements such as Sub-Zeros scar, Kitanas spell, etc are not cannon.