TL;DR: Optional missions are randomly found in the Clockworks. They must be activated by speaking to an NPC or by activating a switch. They will give you rewards if you finish them, and they can be failed. Or at least, some of them. You get the idea.
These missions should be added in the current mission tab, the one above the “return to heaven/ready room” buttons. I know you can do it, you have done it with the sprites in the Charred Court.

To the actual missions:

Captive prisoners:
Simply, an NPC in the beginning of the level tells you that some knight have been missing in these parts of the clockworks. They were engineers, they were there to study the Clockworks and Gremlins ambushed them. Gremlins wanted them to steal some knowledge from the Spiral Order. If you help them, they may unlock the gremlin stash in this clockwork level!
Fehzor's idea: camp with module. module tells inarticulate things about ambush and captives. there's a gate nearby that unlocks itself.
Every clockworks level has its random party button; the party button of this one, should you choose to accept the mission, will be locked, and another door in the level will open, leading to an arena. Gremlin themed of course, and with dead knight bodies scattered around. Once ended, you rescue the engineers, that tell you that they were ambushed and their escort was wiped out. Then another party button brings you right after the party button you didn’t press before.
Now, here’s the trick: these guys actually die. if they take too many hits, they will do the death animation and disappear. They are equipped with short-fused, high knockback but low damaging bombs, that have huge cooldowns. That means you have to protect them. Something like 3 engineers in each level, but if you save at least one, it will open a locked door near the elevator, with some boxes to boost your profit. if you save more, more gates are in the level that the first one unlocks.

Mysterious switch:
At some point in a level, you come across a mysterious board with a switch on it. You don’t know what does this do, but it’s worth a try.
It triggers an alternate path, similar to the previous optional mission. This path brings you to a construct-themed puzzle, and a stash of boxes if you complete it. I was thinking about something like the twisted path with lots of turrets, spikes and brute class enemies, but with some indestructible blocks in the way, and more turrets, and respawining turrets. Maybe some falling rockets like the Collector mission. Lots of bullets on the screen is good for your reflexes, or you could simply kill some turrets before they spot you.
If OOO would also add a Tortodrone something in the level, it would be all worthwhile.

Dark council:
Just before the party button of a devilite workplace level, there would be a sign: “The Dark Council of this section is meeting in a room nearby. If you are one of the Dark Council, press this button, then go explain to the Council why you were late. If you are not a member of the Dark Council, you had better get back to work before your pit boss discovers you.” You had better investigate on this meeting, great devilite administrators could be there!
You go off course to a large room with a great table at the center. A great table with chairs nearby. The party button (and the way you use to get in it) is at one of the corners. Lower corners would be better for this next part. A yellow, black dressed yesman would be there, near the table but away from you. As you step on the party button, it spots you, jumps away to a little table with a phone on it, and picks it up. Timed battle begins! You are lucky that devilite bureaucracy is a mess, you will have 5-3 minutes. It’s a fiend arena.
The yellow yesman position will be shielded by gates. Once you finish the arena, or once time runs out, the gates lower. Now here is the thing:
If you win the battle, use a proto gun to kill the yellow yesman. No, I mean you will OHKO him with any weapon. If time runs out, the yellow yesman transforms into a yellow overtimer, that is like a normal overtimer, but it’s faster, and you still OHKO him.
Also:
If you win, the Council stash is yours! A room with some boxes, and coffee; If you lose, 4 more overtimers will spawn every time you should battle devilites in the level.
If you go near the table, there’s a note: “Council dismissed due to lack of coffee. Remember to bring more coffee from the coffee department on the next Council.”
If OOO would be so gentle to give us Shadow Espresso in this level, that would be great.

Pack Leader's Den:
In a Wolver Den level, somewhere there is an alternate path and a turret. If you inspect the tower, it says: "A large pack of wolvers has been spotted in this area. If any brave knights defeat them, they can take the things that the kleptolisks stole us during our travels here. Good Luck!"
In the following obvious arena, I don't care if you put some respawning wolvers. In fact, you shouldn't. There should be waves and waves of beast of any kind (make sure to insert some kleptolisks in there), like the waves of slags in FSC. The final wave should spawn a wolver pack leader, a bigger wolver with homing bites and more durable buff(s). *insert reward room description here*

Scorched Grounds (T3 only):
Randomly in the level, there should be shadow fires just lying around. At one point, you come across a little fort, with a sign at the entrance: "no beasts of your kind are allowed in Almire!" If you think that the fort is a normal undead arena, you're wrong. The arena layout and the waves should resemble the ones of the final arena of LoA. That should spice up thingies a bit. The reward room should be full of ancient weapons and such, not graves.

That’s all I have for now. Positive feedback? Negative feedback? Destructive criticism? It’s all welcome here. In fact, forget the last thing I said about criticism.