MOPTI, Mali — Deep inside caves, in remote desert bases, in the escarpments and cliff faces of northern Mali, Islamic fighters are burrowing into the earth, erecting a formidable set of defenses to protect what has essentially become Al Qaeda’s new country.

They have used the bulldozers, earth movers, and loaders left behind by fleeing construction crews to dig what residents and local officials describe as an elaborate network of tunnels, trenches, shafts, and ramparts.