By starting a file in BiT as the thunderhead opening cutscene begins to play, you can open the thunderhead on that file before you are supposed to. This trick skips everything between learning Ballad of the Goddess to the Faron Silent Realm, including fighting the Imprisoned and repairing Scrapper.
In order for a file to trigger the thunderhead cutscene in BiT, it must have a specific scene flag: the flag that triggers the thunderhead cutscene on Skyloft is scene flag 2x20: "Play Ballad of the Goddess on top of light tower". Any file that has that scene flag set can trigger the thunderhead cutscene. In the various areas, that flag corresponds to:
To see what 2x20 amount to in other areas, check the Scene Flag Documentation section on the Reverse BiTMagic page.
Once you have such a file, selecting it while in BiT and causing a scene flag change will cause the thunderhead cutscene to play as soon as it can. If your file is saved at a Deep Woods statue, then the cutscene will trigger immediately as you select the file, due to some oddity with Deep Woods. If another dialog or cutscene is playing, the thunderhead cutscene will not play until that one is finished. Things that can delay the thunderhead cutscene include:
The goal is to start the file and then get the Thunderhead cutscene to play during the loading transition. This performs the Story Flag RBM that opens the Thunderhead.
Notes: For some of the following methods, it is required for your file to have the "auto-commit" effect. Usually this is done by saving at any Deep Woods Statue. This is because Deep Woods always has the room 0 zone flag 1x02, which causes an auto-commit in BiT Skyloft (see BiTMagic). The other methods only need to have done one of the events listed above and be saved in that same area.
As soon as you select your file, the thunderhead cutscene is queued, and as soon as the first glitched cutscene is done, it will play. So by loading your file right before the thunderhead cutscene starts, you'll trigger the Early Thunderhead glitch. The window for this trick is about 1 second, as that's how long it takes the screen to completely fade to black after you start your file.
With this method, you will be loaded back at the bird statue you where saved at in the Deep Woods.
If your timing is off while doing this method, the BiTSave will still happen, making the trick difficult to reset. You can try again by going back to the area you where saved at: save, and try again.
When you are not saved in the Deep Woods, selecting your file will not cue the thunderhead cutscene immediately. In that case it is required to BiTMagic the thunderhead cutscene flag in by updating any scene flag in BiT. This is usually simply done by checking the statue you want to BiTSave to with that file. Note that sometimes the file that meets the requirements will have already set the flag corresponding to checking the statue you want to BiTSave to in BiT, and in that case the Thunderhead Cutscene will not trigger and this trick will fail. In that case, either use another statue or BiTMagic the flag with an event that triggers a cutscene, such as opening the shed in BiT. Then go on with the trick following the Deep Woods method instead.
If you didn't see anything special happening after bonking the tree, it can mean one of 3 things:
This method queues the thunderhead cutscene behind the shed-opening cutscene, and will respawn wherever your file is saved, since you did not do a BiTSave. You can then go to the sky and proceed directly to the thunderhead to open the Isle of Songs.
While you do not see the Thunderhead cutscene during the fadeout with this method, it does set the story flag for the Thunderhead to be opened on your file. At the same time it rises the Earth Temple bridge or opens the doors to the Earth Temple in Eldin Volcano.
There are more ways to perform Early Thunderhead that are generally not considered useful, usually due to requiring very long Back in Times, or because the needed setup rarely happens. For exemple you can go to Faron Back in Time in order to use Reverse BiTMagic to set scene flag 2x20 onto Skyloft.
You may have noticed that all the methods above require the file you perform Early Thunderhead on to have scene flag 2x20 in some area. There is one way however to perform Early Thunderhead on a file that does not have scene flag 2x20. The file setup is the following:
Now commit the flag from file 1 and delay the thunderhead cutscene (either by bonking a tree and have the shed cutscene play, or by checking a statue). Then select file 2 and start the file at the correct time. The thunderhead cutscene will still play after you start the file, despite file 2 not having 2x20. This happens because file 1 and file 2 are saved in the same area. See more information about scene flages in BiT here.
Opening up the Thunderhead advances the Headmaster text inside the Academy. This makes you unable to start the quest to repair Scrapper, and thus the quest to retrieve the Windmill Propeller to repair the Village Windmill. This locks you out of every Scrapper-related crystal quests, because one of the triggers for being able to start them is having the Village Windmill repaired. This makes it difficult to perform this sequence break in 100% speedruns.
The Early Boss Rush sequence break can be used to set the Imprisoned 1 as being defeated. However, it also sets the Ancient Cistern as being defeated, which sets Skyview to layer 3. This makes it impossible to talk to the mogma in Skyview 2 to unlock goddess walls, and thus locks you out of the gorko heart piece at Behind the Temple.
There is however one way to skip the Imprisoned 1 fight in 100% speedruns using the Early Thunderhead sequence break, while not getting locked out of any item. To do so, have your run file on File 3, and perform Early Boss Rush on File 1. Then, perform Early Thunderhead on File 1, and fly to the Isle of Songs. Save the game and perform a File Dupe Teleportation (with Bed Trick or Death Trick) to warp File 3 to the Isle of Songs. This allows you to learn Farore's Courage on a file that hasn't opened the Thunderhead. Then, on that file, obtain the Water Dragon Scale and unlock goddess walls in Skyview 2. Then go back to Lanayru Gorge and enter the Imprisoned 1 rematch to set that boss as defeated. You can now talk to the Headmaster, repair Scrapper and the Village Windmill. You can then perform Early Thunderhead again. This skips the Imprisoned 1 fight in 100% speedruns