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At the end of The Avengers, Thor takes Loki as prisoner & also takes the Tessaract, to be placed in Asgard.

But why didn't he also take Loki's sceptre with him?

It was a source of power & mind control which was later revealed to be the Mind Infinity Stone.

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    Maybe because Septor was not Asgard property Tessarect was
    – Ankit Sharma ♦
    Apr 25, 2018 at 15:54

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Because it didn't belong to Asgard

The Tesseract was originally an Asgardian possession and so, rightfully, belonged in Odin's Vault.

The sceptre was NOT an Asgardian possession.., assuming Thor actually knew it had "abilities" separate from the Tesseract (of which there is no indication) let alone that Infinity Stones even existed.

Consequently, it was, apparently, salvaged by S.H.I.E.L.D. and, eventually fell into the hands of HYDRA

The fate of the scepter is covered in This Scepter'd Isle

With the Battle of New York concluded, the Scepter that was used by the Asgardian war criminal Loki is given to S.H.I.E.L.D. scientists Nicholas Cooper and Mark Smith for study. Smith, who abhors his scientific position, is approached by secret HYDRA leader Wolfgang von Strucker to join HYDRA, which is working within S.H.I.E.L.D. Accepting Strucker's offer, Smith steals the scepter and kills Cooper, bringing it to Strucker's facility in Sokovia, a European country embroiled in constant conflict.

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  • If I may ask, why didn't Odin retrieve or send someone to retrieve the Tesseract when Red Skull used it in The First Avenger to produce weapons.
    – KharoBangdo
    Apr 26, 2018 at 5:18
  • @Kharo that's an entirely different question. You should ask it if it's not already asked. Comments are not the right place.
    – M.A.R.
    Apr 26, 2018 at 18:29
  • @Paulie D Though it's not Asgardian property Thor could have taken it seeing it has great powers and SHIELD could use it for making weapons as with Tesseract.
    – iamgroot
    Dec 10, 2018 at 12:47
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Lokis sceptre was likely left with S.H.I.E.L.D for further research at the end of The Avengers.

This is probably because although everyone knew it had mind control capabilities, they did not know it contained an infinity stone itself so it was not in Asgards interest to keep it locked away like the Tesseract.

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