OK, so Warp has a point in it not being able to be in the core. So I was thinking of putting it as a new section of the clockworks that was recently discovered. It could be a new gate in the arcade, like the randomly generated gates from the minerals. there would be 2 free roam gates and 2 standard gates open at any one time, both reacting from haven to the arcade. However, free roam gates would only have 3 floors in each tier, and each be as large as 2-3 floors. on the last floor in a tier, there would be a section on the floor that houses various bosses specific to that tier(it would be helpful if one more T3 and T1 boss was added for this update, to even out each tier). The only gates leading down to the next floor would be found behind the area with the bosses, so you would have to defeat it to go to the next tier. There would also be a basil area found on the second floor of each tier. Since each floor would automatically have every type of monster in it, using minerals to generate it would only change the status ailment of each stratum, like poison or fire. The status of the final floor in a tier is changeable, but it does not affect the status of the boss area(there will be a picture of the floor that will tell you which boss it is in the gate map, just like before but it will now have a background color to tell the status of the floor around the boss). This set-up allows a gate to have one boss of every tier in the gate that has to be defeated to go on, although if this sounds excessive im open to alternate suggestions on which bosses come up in which gate. As warp said before, the maximum number of players that can join a single party will be a multiple of 4, possibly 8 or 12. Each floor also has a small chance of spawning an area on the second floor of a tier containing special mini bosses. T1 could have the Collector from this recent pet update or the Jelly Green Giant(i've never actually seen this monster, so if its not appropriate for T1 then please tell me). T2 could have some kind of new gremlin monster, possibly the giant flame grem from the C42 danger mission or a new fiend based mini boss, possibly Arkus from the mission. T3 would have a Tortodrone (assuming he is a beast) or a new undead mini boss possibly something dealing with a giant kat or Grimalkin monster. Each of these mini bosses/monsters are optional to fight if they are found, but may yield special drops when defeated.
More ideas and refinements to be added at a later date, if you have anything to add please feel free to do so.
This is actually not a bad idea. The fact that you suggested it as a way to get to the Core kind of dooms it though. I'm pretty sure that Nick or someone posted that the Core will never open, because then they would sort of have to end the game with the Knights using the Core's power to get back to their home planet. I do rather like the idea of the Core being a "bonus round" to reward players for reaching Depth 29 from the Arcade, though. Another way to incorporate this without actually opening the Core would be to make the free-roam mode be the shell around the core, with things like the Jelly Green Giant, Tortodrones, and the special gremlins from Operation Crimson Hammer. Also, the maximum knights for the instance should be a multiple of 4.
If you do want to open the Core, this could be included as a special level accessible without reaching Depth 29. Let's call it an "Event Gate." This kind of gate would work as it did during the Preview Events, with each stratum requiring a certain amount of minerals to lock in. Each stratum would represent a single floor of the free-roam level. The final stratum would be a battle against the Swarm as it attempts to corrupt the Core, possibly with the Core entity and/or the Alpha Squad making an appearance. When the players win, the Swarm makes one final strike at the Core, placing it into stasis. Everything still works, it just can't be dug out and plugged into the Skylark anymore. Before the stasis takes hold, the Core entity would make some final encouraging statement about how the Core can still be freed; it'll just take more minerals. EverQuest did something similar (minus the "players win" part) with Kerathyrm the Sleeper. It would also be a good way to end the game, when things come to that. I'd also like to see that sweet "Race to the Core!" stratum thingy put to good use at some point.