We're in a (long) process of reconfiguring the existing rail network to move more lines to through-routing.
Here's the way existing lines operate:
[all black lines on this map and one below are the regional services which run beyond Melbourne]
The City Loop (Flinders St / Southern Cross / Flagstaff / Melbourne Central / Parliament) has 4 individual single track tunnels which allow trains to turnback through a loop (not in and out reverse from flinders street).
All lines used to be associated with one track loop back in the 0s when the three underground stations opened (Flag/Melb Cent/Parly) but over come as frequencies have needed to be increased there hasnt been enough capacity so some lines have been progressively been taken out of the loop and run direct to Flinders Street - good examle is Sandringham on that ma above and Frankston only runs via loop in peaks but also has "shrot stopper" services which run direct and out to stations like Cheltenham (as there's triplicate track in this part).
This map is from 2013 proposals, much of them still on the cards but there are dramatic changes, this is a projection for in 20 years time:
Of the 4 city loop tunnels, only 2 will remain as a loop-turnback. the other two tracks are going to be reconfigured so that they become a track pair for a North-South Line (yellow) which is the existing Craigieburn and Frankston lines.
The blue line is a completely new track pair right through the middle of the city - that's the Melbourne Metro project (all the planning / approvals is getting done now and with a new PM who loves PT in Canberra now, likely to get funding - woo!) - and it's going to combine 3 existing lines (Pakenham/Cranbourne and Sunbury) and provide space for 3 more branches - but in effect it's going to be a massively long line - near on 100km from Pakenham to Sunbury.
The two tracks over the viaducts infront of the CBD which wont be part of the loop-turnback structure that currently exists (thanks to the yellow line now just running through the track pair in tunnels around the edge of the cbd) will be re-used to through-route the Alamein and Glen Waverley lines to the South West lines/branches.
And the Grey line - Mernda (currently runs as far as South Morang) will have a new tunnel from Clifton Hill to Fishermans Bend built - which conceivably (And should) reach Newport at least for connectivity to the west - essentially taken one branch from an exsiting loop-turnback and through-routing it across the city.
The deep purple line will be another north-south line - using for the most part existing track - just with some new flyovers / reconfiguring in the inner north of the city.
There are 4 stages (last map is the 4th stage), you can see the sequencing across all the phases here:
https://urban.melbourne/forum/ptvs-n...ropolitan-rail