Hi, @Teo Kav
Since your friend is not trying to recover the account and mainly wants Microsoft to investigate the compromised account, they can submit a report through Microsoft Digital Safety using the "Report a concern" form: Microsoft Digital Safety https://www.microsoft.com/digitalsafety/report-a-concern
They can select the category that best matches what happened, such as "Fraud and Scams," "Virus, Spyware, or Malware," or "Other Terms of Use Violation," and explain that the Microsoft account was taken over, the sign-in email was changed, and the attacker enabled two-step verification. Microsoft reviews these reports and can take action if its policies were violated.
If you haven’t tried it yet, first make sure the affected computer has also been fully scanned for malware. Microsoft recommends doing this when an account has been compromised, especially since you mentioned that authentication tokens may have been stolen.
I really hope this information is helpful!
Should you need further information, please let me know.
Thanks!