While discussing with Shadow Roxas about Zinnia's Back story the conclusion is that her
husband was already dead for a few years for unknown reasons. Not before Zinnia and her unnamed husband had their daughter Aster. With her husband dead (due to unknown reasons) Zinnia would dote on her daughter Aster, however she was killed off in some manner familiar in a previous game.
Now as you all know in XY Lysandre activated a weapon that could possibly be the one mentioned in the ORAS, and possibly was able to hit some of the Hoenn region, which caught Zinnia's daughter Aster thus killing her. With this loss she decided to project her affections on a whismur to cope with this tragic event.
NOW this brings us to the event of Team Aqua/Magma who she joins up to revive the primal pokemon Groudon and Kyogre so that Rayquaza could be awakened to destroy the meteor. That failing put a hole in the plans of Zinnia, however she was able to find a way around that with the Key Stones. Skip to the Sky Pillar she was willing to sacrifice herself for Rayquaza to save Hoenn, however she gets to live in the end, and at the end of the episode she goes off to who knows where.