First route is the mostly a default option* noted by the Doncaster Rail study and implemented into the PTV plan. Runs mostly along Alexander Parade. *Includes Victoria Market station, not in original plan
The second route option is the future Mernda line diverting at the bend just before Russell station, heads along the Inner circle alignment, and joining the Upfield line near the zoo and then goes to Parkville and Flagstaff (same as default option except with the inclusion of Victoria Market station). There is additionally an option to have a new interchange with the Hurstbridge line as well, as the future Mernda line would divert before connecting at Clifton Hill.
The third route option is similar to the one I discussed on Railpage in March, but has been altered. It runs to Clifton Hill and Victoria Park so can interchange with future Doncaster rail and then diverts and goes through central shopping strips at Fitzroy and Carlton afterward joins at Parkville. Then has a station near the North Melbourne district, and then stopping at Flagstaff.
Link to the map: https://www.google.com/maps/d/u/0/edit?hl=en&authuser=0&mid=1TWDY6V8oWp-pAxYeKgkJHpAzVzg&ll=-37.79549559687072%2C144.97725965000006&z=14