They were definitely stated to be Takeda's bones.

And said bones were a symbolic gesture. The game's backstory establishes that Takeda had been alive and died centuries ago. What Quan Chi did was slaughter the Shirai Ryu (and yes, he absolutely could kill them all in one day, he's the most powerful sorcerer in the MK universe and they're just a village full of peasants), then dig up the grave of their creator and bring his remains to the Lin Kuei as a trophy.

"Scorpion and Batman...family ties?"

My reaction was immediately; "Hell NO".

I'm not ever a Scorpion fan and I don't like that idea. No way man..

Batman's parents and Scorpion's clan are what make them a little similar, but that's it.

... Takeda was nonsense from MK: Conquest...
Where exactly was all this supposed to have been established?...

MK: Mythologies.

Are you sure?... I don't remember any mention of a Takeda...
... And I do remember MKM establishing Sub-Zero murdering Scorpion, and Quan Chi wiping out the Shirai-Ryu.
Sure, he presents one set of bones to the Lin Kuei grandmaster, but they quite clearly refer to him wiping out the whole clan in one fell swoop.

A fact that's continued through to MK4 where that fact is finally revealed to Scorpion and we start the whole chapter of his feud with Quan Chi.

From the instruction manual:
Spread throughout Japan; the Ninja exist as the Lin Kuei's Japanese counterpart. It is believed that a renegade, Japanese-born Lin Kuei warrior named Takeda developed the art of Ninjutsu hundreds of years ago. He returned to Japan to offer his services and knowledge to various lords and generals during that country's feudal period. Many of his skills and techniques were soon copied and learned throughout his homeland. Although the art of Ninjutsu is not based on an individual warriors mutated power, the ninja made up for it with their use of weapons and collective magical techniques that most humans could master with enough practice.

The Ninja have never existed as one collected clan. They work as a loosely connected spy network, made up of several small clans. One such clan is known as the Shirai Ryu. Their founder was Takeda himself, making the Shirai Ryu the very first ninja clan. This also made them instant foes of the Lin Kuei and made Takeda a target for assassination. But, he managed to elude his attackers until his elder years, when he died not from a vicious battle, but in his sleep- a victim of poison slipped into his tea.

Oh, that actually rings a bell now!
Cheers for the info! Nice work!

Yes, while all that is true about Takeda being the founder of the Shirai Ryu, he died hundreds of years ago. The bones that Quan Chi brought in from MK Mythologies were from the current unnamed leader of Scorpion's ninja clan.

Ahh, makes sense now. They never technically said that in the game concerning Tekada, but the booklet confirms it. I'd rather see Scorpion become the Leader of the Shirai Ryu anyway at this point. We'll see in MK8