If you and your players are new to magic, I'd suggest starting out simple. The big story arcs are great, but sometimes they can take over the whole game - which isn't always as fun for the non-magical players of the group.
A few starter ideas:
* Wizkid gang --- either your hired to deal with them, or you run into one during a run
* Reagents have been mentioned already - but just gathering some for a local talismonger from even the the Barrens can be an opportunity to run across para-critters or deal with blighted areas
* free or wild spirits on the loose -- random encounter or hired to deal with
* Just adding magic opposition in your standard runs - an embedded combat mage, wards, a spirit or two, watchers etc.
* Since you have an investigator type, they could be hired to survey a scene by one of their contacts - I always like the 'magic hardboiled detective/gumshoe' concept
* Tracing an astral signature (similar to the suggested track a meat body suggestion by Raven2049 -- good suggestion!

) or erasing your signature (or failing to do so successfully!)
This will let you see what works and what doesn't without having a TPK. Magic can be suddenly brutal with a few bad rolls - it's easy to over power it, as soon as your characters start taking drain, they get to the point where - "hey a gun is not such a bad idea!"

Starting small let's you get all the bugs worked out -- speaking of which, you can then step up to more advanced magic plots:
* Insect spirits are still around, just a little more subtle - I always find it interesting to have one insect faction hire runners to go after another faction
* Free spirit that is a fixer/Johnson - motivations can run the gamut
* Toxic mage/shaman or Blood mage - bounties - just keep in mind that they can be incredibly tough!
* Portals and astral rifts ---- they are great! The results are completely up to you - very open ended - though can get cheesy if you aren't careful.
* Magical groups - check out the different resources out there, Street Grimoire, Threats, Threats 2, Magical Societies etc.
* Shedim - less common to some degree, but could still be a good story arc
* Shadow spirits have been mentioned - but also a longer arc potentially
* Geomancy - helping to re-align ley lines, definitely can have unintended affects
* Dragon driven plot - long, convoluted, and often fatal!
There are also tons of runs out there if you want to sift through -
I always have liked
Bottled Demon - it would need to be updated for 5th edition.
The first run in
Firing Line has a cool run that has a magical spin. Could easily have a spinoff later.
If you want to amp up the creepy factor, read through
Universal Brotherhood --- probably not one you want to do since it is based in 2050s, but great for getting ideas and seeing how things came to be.
Ghost Cartel and the Artifact series of runs would also have heavy magical related runs -- but are both pre 5th, so depends if you want to work with current story arcs.
I'll stop now.
