EDIT: Possible alternative final boss after Kri'unh or Hardmode only Boss. Primus Cas'ul. After defeating Kri'unh, you hear the same voice over an intercom throughout the ship and the jamming device in the room shuts off. A huge door (similar to the one one the spire mission on Mars, but on a much larger scale) begins to open in the back of the room leading to an enormous room with more of the jamming device and the Cabal leader of the ship Primus Cas'ul. The room is very long with an oval shape to it, and spread out around the room are 6 jamming devices as well as pipes across the walls and very little cover to hide behind. The fight will star with Cas'ul, a very large Colossus style model with 2 miniguns, one in each hand, start the devices while standing on a platform above the room, and protected behind a force field or some sort of glass inclosure.

The devices, like in Kri'unh's room, will disrupt the Guardians abilities and weapons making them useless while active. The 6 devices in this room however have control panels located on them that, if all hit within 3 seconds of the first being activated, will turn them all off for a short period of time (one minute). After they have all been disabled, 3 phalanx and 1 centurion will spawn. The Phalanx and Centurion must be dealt with as they have before, using team work and environmental effects from shooting the pipes to bring them down. The Centurions hammer can be picked up by 1 guardian and used to destroy one of the devices. Destroying the device with the hammer will also destroy the hammer as well. When a device is destroyed it will leave a path of fire around it forcing guardians to not be able to stand in that area any longer.

Once you have the destroyed one device an automated defense system will kick in and shoot at the guardians forcing them to take cover and keep moving (turrets from the ceiling with rockets and/or chain guns). After 30 seconds the defense system will shut itself off and the guardians can once again disable the devices, this time causing 2 centurions to spawn, leaving 2 hammers. Repeat the same phase over, disable the remaining 3 devices and 3 centurions will spawn. Once all devices have been destroyed Cas'ul will enter the room from his perch and begin engaging the guardians.

With the edges of the room filled with fire your previous cover from the turrets can no longer be used, and at this point you will be able to pick up a previously killed Phalanx's shield and slam it into the ground using your melee button to create a barrier. Multiple shields can be placed to create a larger barrier. These shields will not withstand Cas'ul's fire for very long, and Phalanx will occasionally spawn allowing you to kill them and keep your barrier up.

Cas'ul will be covered in the same bullet proof armor and only his weapons will be able to be destroyed at the start. Upon destroying both of his weapons his armor will be weakend and you can do damage to him directly. Once his weapons are destroyed he will leap back up to his perch and wait while more Phalanx and 5 Centurions flood into the room. After all have been defeated he will come back down, this time with a Phalanx shield and a Cabal Hammer.

You must hit him with the Cabal hammer to briefly stun him and allow your fireteam to unload shots into him while hes not protected with his shield. This will be necessary since tho his armor is weaker, it will still stop most damage, besides his head which is now unprotected. This will encourage precision shots over just firing rockets, and require coordination between the team mate using the Cabal Hammer and the rest of the team to fully exploit him while he is stunned. For 10 seconds after each time he is hit with the hammer he will become enraged and instantly kill anyone coming within melee range, so he will not be able to be stunned.

Again this is just an idea for a seperate ending boss then Kri'unh or a Hardmode only boss. Thanks all for reading and thanks to everyones feed back this far, has really helped with future ideas!