How did the Great Devourer get sealed, and where did the Fang Blades come from?
How can Pythor play the Sacred Flute? We see in Tournament of Elements that Anacondrai are affected by it, just like the other Serpentine, so he should have been affected.
Why did Dr Julien get rid of Zane's memories?
How were the judges so easily fooled by Pythor's disguise?
How did Kai figure out that Lloyd was the Green Ninja?
How did Garmadon get the aid of the Skulkin to fight the Serpentine?
If Zane recorded the music of the Sacred Flute, why didn't he ever use it after the Sacred Flute was stolen?
I don't know how to respond to the other plot holes, and some would only lead to far-fetched theories that'd take too much time to write, but for the ones in bold I'll suggest:
1. I was left with the impression that Dr. Julien had decided that once he was gone, Zane should go out into the world and "protect those who cannot protect themselves", and perhaps he felt that if Zane remembered his old life, he might cling too much to old memories and wants, and it could distract him from what he was built to do.
How did the Great Devourer get sealed, and where did the Fang Blades come from?
How can Pythor play the Sacred Flute? We see in Tournament of Elements that Anacondrai are affected by it, just like the other Serpentine, so he should have been affected.
Why did Dr Julien get rid of Zane's memories?
How were the judges so easily fooled by Pythor's disguise?
How did Kai figure out that Lloyd was the Green Ninja?
How did Garmadon get the aid of the Skulkin to fight the Serpentine?
If Zane recorded the music of the Sacred Flute, why didn't he ever use it after the Sacred Flute was stolen?
I don't know how to respond to the other plot holes, and some would only lead to far-fetched theories that'd take too much time to write, but for the ones in bold I'll suggest:
1. I was left with the impression that Dr. Julien had decided that once he was gone, Zane should go out into the world and "protect those who cannot protect themselves", and perhaps he felt that if Zane remembered his old life, he might cling too much to old memories and wants, and it could distract him from what he was built to do.
I don't know how to respond to the other plot holes, and some would only lead to far-fetched theories that'd take too much time to write, but for the ones in bold I'll suggest:
1. I was left with the impression that Dr. Julien had decided that once he was gone, Zane should go out into the world and "protect those who cannot protect themselves", and perhaps he felt that if Zane remembered his old life, he might cling too much to old memories and wants, and it could distract him from what he was built to do.
2. Because the judges were short-sighted idiots.
1. Alright, that does make sense.
2. So how did they ever get their jobs?
2. I guess because they looked good and knew how to smile for the camera.
How did the Great Devourer get sealed, and where did the Fang Blades come from?
How can Pythor play the Sacred Flute? We see in Tournament of Elements that Anacondrai are affected by it, just like the other Serpentine, so he should have been affected.
Why did Dr Julien get rid of Zane's memories?
How were the judges so easily fooled by Pythor's disguise?
How did Kai figure out that Lloyd was the Green Ninja?
How did Garmadon get the aid of the Skulkin to fight the Serpentine?
If Zane recorded the music of the Sacred Flute, why didn't he ever use it after the Sacred Flute was stolen?
1. I always assumed they somehow chased it underground using the flutes and then put it to sleep somehow. ( Maybe with a spell or something? ) And maybe they were made from it's teeth that feel out, because the blades were side to made from the actual teeth of the Devourer.
2. Ear plugs, he's shown putting them in his ears before he speaks to all the serpentine in Ouroboros.
3. I think it's because he wanted him to live a more normal life.
4. Because 50% of Ninjago's population isn't very smart.
5. Maybe a true potential epiphany.
6. Portal to the Underworld perhaps.
7. In the episode I believe he said he extracted it from his memory database, so maybe it's because he didn't think to do that until then.
I rewatched Day of the Departed, and I can safely call it the special where things just happen without explanation.
Why does Cole start randomly fading away, and why do the ninja just forget him? Did Master Yang do it? If so, how?
What does Yang's cryptic "Close the circle" message mean?
What exactly is the Departed Realm?
Why does Yang bring back the old villains? The ninja don't remember Cole, so he doesn't have any need for them.
How was the Yin Blade recovered?
Why do Kai and Nya wonder where their parents are? Didn't Possession say that they died?
Why is Pythor suddenly evil again?
Where did the RX powers come from?
What's the significance of Cole's ghostly scar?
Honestly, this special might be more nonsensical than Wrong Place, Wrong Time.
2. I don't know, maybe close the circle of events. I kinda wish it were a bigger part of the plot because its an awesome song. Actually, the answer might be in the song... All I got from listening to the song is " bring the rift and close the circle, running out of time "
3. I believe it's supposed to be where all dead characters spend their afterlife. A place that only can be reached by death.
5. Clearstone is the hardest substance known to humans in Ninjago... I'm hurting my mind trying to figure that one out.
7. Maybe he can't make up his mind.
9. Probably a reminder and a remnant.
I have theory that time travel doesn't work the way we would assume it would in Ninjago and maybe there's something that kinda sets things back into place in a strange way when time travel is used. Perhaps something to do with the element of time or Cloud Kingdom or even how Ninjago itself was created. I don't really know though, I haven't had a lot of time think this theory through yet.
How did the Great Devourer get sealed, and where did the Fang Blades come from?
How can Pythor play the Sacred Flute? We see in Tournament of Elements that Anacondrai are affected by it, just like the other Serpentine, so he should have been affected.
Why did Dr Julien get rid of Zane's memories?
How were the judges so easily fooled by Pythor's disguise?
How did Kai figure out that Lloyd was the Green Ninja?
How did Garmadon get the aid of the Skulkin to fight the Serpentine?
If Zane recorded the music of the Sacred Flute, why didn't he ever use it after the Sacred Flute was stolen?
1. I always assumed they somehow chased it underground using the flutes and then put it to sleep somehow. ( Maybe with a spell or something? ) And maybe they were made from it's teeth that feel out, because the blades were side to made from the actual teeth of the Devourer.
2. Ear plugs, he's shown putting them in his ears before he speaks to all the serpentine in Ouroboros.
3. I think it's because he wanted him to live a more normal life.
4. Because 50% of Ninjago's population isn't very smart.
5. Maybe a true potential epiphany.
6. Portal to the Underworld perhaps.
7. In the episode I believe he said he extracted it from his memory database, so maybe it's because he didn't think to do that until then.
I rewatched Day of the Departed, and I can safely call it the special where things just happen without explanation.
Why does Cole start randomly fading away, and why do the ninja just forget him? Did Master Yang do it? If so, how?
What does Yang's cryptic "Close the circle" message mean?
What exactly is the Departed Realm?
Why does Yang bring back the old villains? The ninja don't remember Cole, so he doesn't have any need for them.
How was the Yin Blade recovered?
Why do Kai and Nya wonder where their parents are? Didn't Possession say that they died?
Why is Pythor suddenly evil again?
Where did the RX powers come from?
What's the significance of Cole's ghostly scar?
Honestly, this special might be more nonsensical than Wrong Place, Wrong Time.
2. I don't know, maybe close the circle of events. I kinda wish it were a bigger part of the plot because its an awesome song. Actually, the answer might be in the song... All I got from listening to the song is " bring the rift and close the circle, running out of time "
3. I believe it's supposed to be where all dead characters spend their afterlife. A place that only can be reached by death.
5. Clearstone is the hardest substance known to humans in Ninjago... I'm hurting my mind trying to figure that one out.
7. Maybe he can't make up his mind.
9. Probably a reminder and a remnant.
I have theory that time travel doesn't work the way we would assume it would in Ninjago and maybe there's something that kinda sets things back into place in a strange way when time travel is used. Perhaps something to do with the element of time or Cloud Kingdom or even how Ninjago itself was created. I don't really know though, I haven't had a lot of time think this theory through yet.
3. That is pretty obvious, but what kind of realm of the dead is it? What's the difference to the Underworld and Cursed Realm?
2. I don't know, maybe close the circle of events. I kinda wish it were a bigger part of the plot because its an awesome song. Actually, the answer might be in the song... All I got from listening to the song is " bring the rift and close the circle, running out of time "
3. I believe it's supposed to be where all dead characters spend their afterlife. A place that only can be reached by death.
5. Clearstone is the hardest substance known to humans in Ninjago... I'm hurting my mind trying to figure that one out.
7. Maybe he can't make up his mind.
9. Probably a reminder and a remnant.
I have theory that time travel doesn't work the way we would assume it would in Ninjago and maybe there's something that kinda sets things back into place in a strange way when time travel is used. Perhaps something to do with the element of time or Cloud Kingdom or even how Ninjago itself was created. I don't really know though, I haven't had a lot of time think this theory through yet.
3. That is pretty obvious, but what kind of realm of the dead is it? What's the difference to the Underworld and Cursed Realm?
I'm assuming the Underworld and Cursed Realm (until it was destroyed) were where the bad people went. But then how did Wu get to the Underworld in the pilot episode...? Future plot idea, anyone?
Has anyone talked about the Wrong Place, Wrong Time Plot Holes?
Alright, let's see which makes less sense. Wrong Place, Wrong Time, or Day of the Departed.
How did Garmadon go to the Realm of Madness and get four arms?
How did the ninja retrieve the Fangpyre Staff and cure Ed and Edna? They wouldn't have had their 2012 vehicles.
How was the Great Devourer destroyed?
How did Lloyd grow old?
How do the pirates still exist in Skybound?
On second thought, Wrong Place, Wrong Time is much more nonsensical than Day of the Departed.
What I'm about to use for answering your questions is pure theory (because this isn't canonly, for lack of a better word, explained), but I will attempt to answer as best I can.
1. He did know about Mistaké's traveler's tea.
2. They still had the anti-snake flute.
3. ...no answer.
4. Garmadon got Nahdakhan to make the Grundal old and the rest of the events carried out? But Garmadon was wise enough to wish for Nahdakhan to go back in his lamp? Again, theory.
5. I'm not sure I understand the question...And how would that be affected by Wrong Place, Wrong Time again?
All I got from listening to the song is " bring the rift and close the circle, running out of time " 
