What if the true final boss was the very Core itself? Here's some scenarios...

All of the scenarios involve the Core finally being unlocked, but something goes wrong...

1. The Core - The Core turns into a very large Knight or robot and kills most of the Knights in the Core room with one or more survivors sending the distress call before they too are killed from the menace. NPC Knights with 5* gear rush in to assist you and your squad. 8 players can be in the instance. Alpha Squad appears on the scene with a weapon from the Skylark and helps you blast it to smithereens when Phase 3 rolls around. Rhendon appears in Phase 4. Phase 5 involves TWO copies of the boss, with damage and defense increase. Phase 6 is the end of the boss, both copies exploding into nothing but dust.

2. Corrupted Alpha Squad - Alpha Squad themselves appear in the core, but corrupted like that guy from Mission 9-1 (3), except the Alpha Squad's armor is very damaged and cracked, their power has increased tenfold, and they will MURDER you. They have killed almost all of the Knights in the Core with ease, a distress call is sent before the remaining survivors are killed. You are sent in with anyone else you can get in touch with. Rhendon and many other NPC Knights with 5* gear are in the area to assist you in defeating Alpha Squad. Their curse is lifted once they are knocked out for good after 4-5 phases, and they awaken, all normal. Attack increases per phase, Defense decreases per phase until Phase 3 where it increases, but attack decreases.

3. Corrupted Herex - Herex himself activated the Core on purpose instead of energy coming down to the Core, and has harnessed the energy in the Core to turn himself giant and with unspeakable power, kills all of the Knights in the Core room. Kora is suspicious of the sudden radio drop and sends you and a squad of 6 Knights in to see what the problem is. 5* NPC Knights assist you in the mission. Rhendon is on the scene when you get there. Phase 2 occurs when you do 1/4 of his HP, and Herex suddenly gains a mutation, suddenly the Swarm appearing and corrupting his body. He has Curse weapons and armor on, wielding a giant halberd and can throw Shadow bombs at you. Phase 3, and he finally explodes, flying into the Core and being destroyed for good.

4. The Swarm leaks into the Core room, kills the Knights in the room, and corrupts the Core, creating a enchanced version of the Collector, except with way more deadly weapons and will MURDER you if you aren't prepared. 10 Knights can be in the instance and 5* NPC Knights will assist you. Energy Turrets are scattered around the room, placed before the Swarm came in. Phase 2, the Swarm becomes enraged and creates 2 copies of the boss, however with less HP than Phase 1. Their attack is also lessened. Phase 3, and an army of these bosses appear, and when you look like you're about to die, an explosion sends them all back. A weapon from the Skylark had blown most of them to smithereens, with Alpha Squad manning the cannon. The boss turns into a more giant version of itself, gathering energy from the copies. Once destroyed, the boss explodes and is dead.

5. Elite squads of Gremlins of the Crimson Order host a raiding party on the Core room, kill the Knights in there, and attempt to activate the core themselves. Kora sends you and a squad of 8-10 Knights to investigate. Once you're in there, however, all of the Gremlins are strangely dead. By the time you reach the balcony to look at the Core, it has turned into a gigantic robot armed with a deadly array of weapons meant to kill anyone with brutal force and ease. You can't damage the robot a lot, and when Phase 2 occurs, Alpha Squad has suddenly appeared on the scene, armed with a weapon from the Skylark, setting it down on a makeshift tower, blasting at the boss. Phase 3 occurs, the boss destroys the tower, but doesn't kill Alpha Squad. They, however, are seriously wounded, and you must man the cannon to make the finishing blow on the boss. If you're too slow to hit all the targets, you are instantly KO'd and the cannon must recharge before another player can have a try to kill the boss. Phase 4 involves the boss exploding for good.

Shadow Lair Bosses

1. Shadow Alpha Squad - A brutal version of Corrupted Alpha Squad. 12 Knights can be in the instance. No NPC help. However, the Shadow clones disappear instead of turning back to normal Alpha Squad. Sanctuary entry upon defeat.

2. Shadow Herex - A more brutal verison of Corrupted Herex. Same outcome as Corrupted Herex. Sanctuary entry upon defeat.

3. Shadow Core - A very brutal version that is like a prepare-to-die verison of The Core. The Core deactivates upon defeat, and explodes, however you end up at the Sanctuary instead of being a smoldering pile of ash.

4. Shadow Arkus - The living, strong soul of Arkus survived after being killed by you back at Mission 9-1 (3). The fallen members of his squad have been corrupted by the Swarm, and now his revived squad will take revenge on you for killing Arkus. 8 Knights can be in the instance. The squad thanks you for removing their curse upon death, and their spirits are free. You are taken to the Sanctuary upon boss defeat.

If any of these bosses are defeated (except Shadow Lair bosses) Kora thanks you for finally securing the Core. A cutscene is shown afterward of a time lapse after Knights gather energy from the Core and fueling it to a now-rebuilt Skylark. All of the Knights on Cradle are taken back to Isora, only to find it overrun by their enemies from the Morai Wars. Or not, depending.
This is only a Suggestion(s). And several ideas. Thank you for reading.