City resources are managed by constructing "modules" very much like the Space Cities from CTP (the module adds a bunch of food/shields/trade to a tile that normally has none). That requires underground space to be Excavated by an Excavator unit.
Excavation produces Tunnels which are built much like the underwater canals. A tile is selected for tunneling and an excavator unit goes to work on it, transforming it into a tunnel in 2 or 3 turns depending on technology.
Tunnels excavated around the City allow movement of units as well as space to build Modules to support the city.
Exit Points to the surface can be built just like Tunnels.
(and well, you could make a unit that even has an underground movement speed, just like drill-tanks
)Modules can be pillaged, and Tunnels can be pillaged (moves the unit to an adjacent tile) but this only produces a Rubble Tile in the Tunnel which impedes movement (Rubble Tiles can be cleared in 1 turn by an Excavator).
Railroads and Maglev can be built in Tunnels. Tunnels do not grant movement benefits like a road but they fulfill the requirement for rail and mag. You cannot built a road in a tunnel. It does count as Mountain movement for units which are unable to move through mountains (such as tanks) until it gets a mobility improvement.
Exit Points can have a regular city built on top of them, or can be constructed in a space where a city already exists. However they can be built in any place that is not covered by water (and with sufficient tech, you can make them open up in ocean tiles too).
However any units attempting to move from Underground to the Surface layer in the City invoke combat if the city isnt yours. So you can excavate a tunnel under an enemy city and open an Exit Point under their city to attack them from underground, but its a fight just like any other, and by doing so you also open up your tunnel network to them sending units downstairs too.
The counterbalance to the attack advantage this gives (unless there are high tech units with See Underground flags), is that the expansion underground takes time just like building railroads above ground, and underground the movement paths are limited and enemy units encountered underground can be cornered and forced to fight. And there probably shouldn't be any variable terrain adjustments underground to movement or defense (just as on the ocean there arent any).
Except for units who have See Underground flags (if it would exist) all units who are underground have no vision range, and can only see their own space (tunnel movement options are implied based on tileset graphics). But if you try to move into a square that has an enemy unit you are stopped and they are revealed like it usually is with stealth units.
Naturally, all underground tunnels you've been through remain in the fog of war.
This is inspired by Fallout, and the covert DUMBs theory (deep underground military bases).
Not to mention in a Fantasy game setting it would be important to have for Dwarves/Orcs/Goblins, which would make it alot more fun to find out that there is a "whole nother map" of gameplay going on at the same time. In a fantasy setting some races could get that technology to start with so its not necessarily a late-game feature.