Get ready for the longest,biggest, most useless post of your life everyone:
We all react with ''HOW DA FK DID HE USE NINJUTSU BEFORE ME!!!!'' when the enemy gets to use ninjutsu 1st. Today i'm hoping my explanation can help you understand that factors that decide who goes 1st. I'd also appreciate if someone could make an easier to understand version with less text about it because I don't know of another way to explain it.
This here is your Battlefield:
7 4 1
8 5 2
9 6 3
According to where you have your characters at, it will decide who gets to attack first. The smaller the number the faster your character will attack. Meaning if your character is in position ''1'' he'll attack faster than the enemy in position ''2''. Let's say one of you characters is at position ''1'' and one of the enemy characters is at position ''1'', In that case whoever has the ''lightest'' attack attacks 1st, Fire's sleeping normal attack is ''lighter'' to all the standard attacks in the game,that's why he'll always go 1st before the enemy, However, if the refinment difference between the 2 characters are huge then the enemy will go 1st. Refinement doesn't play a big role as much as the position of your character and type of attacks used. So The position and type of attack decides who attacks 1st, the position is more important when it's just normal attacks.
As for ninjutstu, Someone in position ''1'' will activate it faster than someone in position ''2'' However, unlike normal attacks, some ninjutsu takes priority over others. Let's assume you have shikamaru at position ''9'', And the enemy character activating ninjutsu is at position ''1'', Shikamaru will then activate ninjutstu 1st. As i said before, the position AND type of ninjutsu determines who uses ninjutstu 1st, Shikamaru causes immobalize which takes priority over every other ninjutsu in the game because it's the second ''lightest'' ninjutsu in the game. Area changing ninjutsu like Haku,Sasuke and Anko have 2 stages. 1st stage is where you change the enviroment which takes normal priority, meaning if it's activates in position ''2'' and the enemy activates a ninjutstu in position ''1'' then the enemy will use ninjutstu first. The 2nd part of the move though,the one that requires 40 chakra which deals damage, that is the ''lightest'' ninjutsu in the game and is the only ninjutsu type faster than shikamaru's immobalize. The Fire's Seal mystery takes 3rd fastest priority in the game, being slower than shikamaru's immobalize and enviroment changing mysteries. Now note, Shikamaru's mystery isn't the fastest in the game, shikamaru's ninjutsu ''type'' is the fastest in the game. Meaning Zabuza (hidden mist unit)'s mystery causes immobalize to the enemy, Therefore, it's also the 2nd fastest ninjutsu to be activated, being slower than enviroment chaning mystery (2nd part). As to how to know what ninjutsu ''type'' is the ''lightest'' and fastest, You'll have to get a feel of it as you play. Lightning's Chidori blade seems to be a little lighter than other area attack mysteries for some reason, which is why if he's in position ''1'' and fire uses dragon flame jutsu while also in position ''1'' chidori blade will always activate 1st, unless the refinement difference is too big.
1 last thing, If an enemy uses ninjutsu, and you use immobalize or seal on him 2 seconds before his ninjutsu activates, he'll get the 1st move, there's a small delay in the game, so even though you activated immobalize 2 secs before his ninjutsu activates, to the game, it'll be considered you activated immobalize AFTER his ninjutsu was in effect, So you need to either guess who's gonna use the ninjutsu or be quick enough to immobalize him, Alternatively If you set the game to Auto, It'll automatically immobalize,seal,interrupt etc... any enemy using ninjutsu without u have to guess, however that also means it'll activate the other mysteries you have on randoms, so it's best to use other mysteries 1st then set it to auto for the immobalize,seal etc.. then return it back to normal.
Congratulations if you managed to read through all that long text and understand my explanation, i'm not the best at explaining stuff like this so some things might be unclear here and there.