I want you guys to picture something with me.
A team of capsuleers take an activation gate into a plex or high level mission. There, behold, is the enemy command ship. It activates specialized hardening systems, similar to those on a POS, preventing the capsuleers from damaging it. While most deal with the smaller ships defending the command ship, one activates a specialized electronic warfare module which hacks clone modules on the ship, allowing friendly mercs to activate their own clones on board. As the mercs advance against the defending bots (be they drones, sansha, or whatever) they capture an objective, disabling the hardener. They then attempt to hold that position while the capsuleers, still dealing with the command ship's minions, take advantage of this moment of vulnerability to break through the command ship's shields.
Finally, the command ship begins taking armor damage. Oh no, it has a second hardening system for its armor! The mercs advance again, traversing everything from cramped hallways, to barracks, to massive open hangars containing deployable drones and packaged ships, to reach and hack the second hardener. They hack it, and again must hold it until the capsuleers can destroy the ship's armor.
As the command ship begins taking hull damage its commanders accept defeat and decide to take the boarders down with them. A self destruct sequence has been activated. Our mercs are faced with a choice: head back where they started and hope to escape before the ship goes up? Or move for the CIC, defeat the commanders and their elite guards, and hack the ship's computers to stop the self destruct, thus allowing better loot and salvage, and perhaps a WP/SP bonus to all involved.