As a casual viewer, you would be forgiven for thinking the 10ACraft plot just takes place episode after episode, and for the most part, it kinda does. However, there are certain episodes that just don't fit into this idea, so here is that we think the tineline would look like, applying the clues we've been given.
Note: This has not been confirmed by TheSuperArtistGamer or any associates. This is purely speculation.
Spoilers have been left unmarked. You have been warned.
This is the timeline that occurs before 10A enter the Minecraft Realm. The Five Nights at Freddy's 2 Episodes and 10A Shorts are generally thought to go here.
Ignoring the animating engine for the sake of evidence (it's only an engine, after all), these events are assumed to take place in the real world. This is implied by the lack of comic violence in these episodes, and, in the case of the Five Nights at Freddy's 2 episodes, how the injuries the gang sustain have a much more serious atmosphere to them.
In addition, 10A Shorts appears to focus on the school life of the characters; the fact that their old lives have been abandoned since the gang's entering of the Minecraft World implies that school doesn't exist there (not in the same fashion, at least). This further proves that 10A Shorts takes place in this timeline.
As for the Five Nights at Freddy's 2 Story Arc, the conclusion many fans tend to make is, assuming this story arc is parallel to the Five Nights at Freddy's games, that these episodes serve as prequels to the Five Nights at Freddy's arc of Season 1. This is backed up with Alex W's role in the episodes: In F Na F 2, he is physically absent. In F Na F 1, however, he gets introduced to the class and he becomes one of the family.
In regards to the order, using (possible) evidence, we can conclude that the FNAF 2 episodes take place before 10A Shorts: Episode 1. Throughout the FNAF 2 trilogy, there's the absence of one major character: Kyle C. In addition, when Ross and Rebecca stumble across a class photo from when the class were in 8A, Kyle was oddly absent (Charley and Alex W were notably present). In 10A Shorts, Kyle C DOES make an appearance, which could imply that Kyle, like Alex and eventually Ryan, Rory and Haleema, only joined the class later on. This is purely speculation, though.
This timeline officially ends when the gang enter Minecraft just before the events of Season 1, Episode 1. The Super Artist Gamer basically confirms this in an Update Video.
This timeline is a lot more straightforward, although the introduction of Alex W tends to complicate things somewhat. It is stated in Episode 4 that Alex joins the class, however his introduction is very delibrate and to-the-point. Alex's backstory, however, gets developed in Episodes 14 and 15, and it wasn't until Episode 15 where a formal introduction was made. Hense, it is generally accepted that the F Na F 1 Episodes take place after the events of Episode 3 (where Alex was absent) and before Episode 4 (BAM! New character).
Some episodes could also be out of order in terms of development: notably, the Football episodes in Season 1 are episodes 16 and 19, getting interrupted by the Christmas episodes. Since the episodes aren't linked, whichever one comes first is debatable, but generally doesn't affect the main plot in any way.
Minigame Episodes are also canon, although there is debate over where they are placed in the timeline. Many fans accept that these episodes take place in order, like the main ones (Total Wipeout takes place after the events of the Q'n'A, for example), although in different worlds that Mr. Coyle (could have) made, which is why each minigame takes place in such a different environment compared to the main series.
What has been confirmed, however, is that, as of Season 2, Episode 16, the class have been in Minecraft for roughly a year, as evidenced by Haleema and Ryan joining 11A (confirmed to be the 10A that are in Minecraft) in 10A Shorts: Episode 3.
It is speculated that 10A Shorts: Episode 3 takes place in the real world somewhere between Season 2, Episodes 15 and 16 in the Minecraft World.
It is worth noting that 10A Shorts: Episode 4 is the only 10A Short that takes place in Minecraft itself, so it's fairly straightforward to place on the timeline. It is speculated to take place sometime after Season 2, Episodes 18 and 19, though whether it's before or after the Season 2 Q'n'A remains uncertain.
This is the timeline that takes place after Minecraft, supposedly. Right now, it is speculated that only one episode goes here: 10A Shorts: Episode 2, which features Ross, Emily, Matthew, Alex D and Sharkey going back to their old school only to find it going up in flames. Even then, how they returned from Minecraft is unknown, especially since, apart from Sharkey and Emily, they all died in the penultimate episode of Season 2.
This episode, in addition, can't have taken place in the Pre-Minecraft Timeline as it has been confirmed that the gang were in school when they went to Minecraft in the first place; therefore it would have to be in habitable condition. Of course, given that the episode in question is based on a real event that happened to Foyle College (thus confirming that the 10ACraft series as a whole is, to an extent, real), the episode could simply be non-canon. Only time will tell.
