dep2.js

module.exports = { test: 2 };

dep.js

var dep2 = require('./dep2'),
    dep3 = require('./dep3');

module.exports.one = { test: 1 };
module.exports.two = dep2;
module.exports.three = dep3;

dep3.js

module.exports = { test: 3 }

index.js

var mr = require('mockrequire');

var dep = mr('./dep', {
  './dep2': { test: 3 }
});

console.log(dep.one);
console.log(dep.two);
console.log(dep.three);