One thing I've noticed on this message board as the Ninjago Fandom has grown, there has always been a slight neglect to what is canon and what is not canon. The purpose of this topic is to clarify what ACTUALLY happened and what was meaningless supplemental material. To start off, here's a basic timeline of Ninjago canon.
TV Series Timeline:
Pilots
Seasons 1-4
Ronin (Similar events to SoR)
Seasons 5-6
Dark Island Trilogy
Day of the Departed
Season 7 and Beyond
Graphic Novel Timeline:
Alternate Pilots
-[Papercutz #1-2]
Alternate Season 1
-[Papercutz #3-5]
Alternate Season 2
-[Papercutz #6-8]
Alternate Season 3
-[Papercutz #9-11]
Ninjago Movie Timeline:
The LEGO Movie
The LEGO Batman Movie
The LEGO Ninjago Movie
The LEGO Movie Sequel
If you have any questions on specific pieces of Ninjago canon, feel free to ask! And if you believe I'm wrong, you can politely counter my arguement.
This is a re-post of a topic on the original LEGO Message Boards
Pilot Episodes: The skeleton army episodes. Originally 2 half-hour episodes, though sometimes split into 4 quarter-hour episodes. I think sometimes it is even shown as a full movie, so whether it is an episode or episodes is kind of debatable.
Pre-series mini-movies: These first aired on Cartoon Network and then appeared on Lego.com and are just some quick 5-minute shorts that take place after the pilot episodes, but before the proper start of the TV series.
Season 1: Rise of the Snakes - The snakes, the Great Devourer, who is the Green Ninja, that stuff. Tells the first part of the 2012 story (the part that most of the sets are based off of), though the season ended way before 2012 did... it ended in April, before the summer wave of sets had even been released!
Season 2: Rise of the Green Ninja - This season is kind of unusual. The first half is mostly just fun filler, essentially being a series of Mega Weapon stories, most of which don't have that much influence on the greater plot. The filler stuff then ends/transitions into the much more story-heavy second half with Child's Play and Wrong Place, Wrong Time. The series went on a month-long pause during September, and then returned in October, which is where I would consider the "second half" to begin. This is where all the Final Battle stuff happens, and the last couple of episodes (starting with The Dark Island) have a noticeable budget increase or something... the animation just looks twice as good as the previous episodes. This season started airing in July 2012, and ended in November 2012. The second half of the season tells the 2013 story, and once again, the season ended before the sets that corresponded to the season were even released.
At this point, Ninjago was supposed to have ended, as it had run its 3-year course, and this is evident by how Season 2 ends. However, due to being unexpectedly popular, Lego decided to extend Ninjago's lifespan, and began working on new sets & story, which would become the Rebooted arc. The Final Battle sets could be considered the sets of 2013, though they were technically released in very late December 2012.
During 2013, Chima (originally intended to be the Ninjago-replacement as the 3-year story-based theme) had its first season, which was 20 episodes long, as opposed to Ninjago's 13-episode seasons. It would then proceed to have a rather short 6 episode season 2 in 2014, however, perfectly balancing out its total # of episodes to 26. And speaking of 2014...
Season 3: Rebooted - The season with the nindroids and all that stuff. Unlike previous seasons, this season was only 8 episodes long. This season was spread out across the entire year of 2014, with 2 episodes being shown back-to-back in January, then April, then July, and finally November. This season seems to take place some time after season 2, though just how long is unknown. One thing that has always bothered me about this season is that the Elemental Blades and the Ultra Dragon both disappear... and despite even being mentioned during the season, no explanation is ever given as to where they went. One thing I've heard is that maybe the Elemental Blades were destroyed at the end of Lloyd VS Overlord battle in season 2, but you can actually see the elemental blades on the ninja's backs at the end of the episode, so who knows what happened to them. I'm pretty sure the Ultra Dragon was still alive, too, so where did it go? I really hope they revisit this at some point and at least explain what happened to them... at least the golden weapons were taken care of, story-wise.
Season 4: Tournament of Elements - Starting with this season and onward, all seasons are 10 episodes long... perhaps because of the other Lego TV shows taking up some o the budget? This is the season where they find Zane, Skylor appears, and all that stuff.
Season 5: Possession - The season with Morro and the introduction of Airjitzu.
Season 6: Skybound - The season with Pirates.
Day of the Departed - A 45-minute special that premiered on October 29, 2016.