Reading this may help you understand the story better.
BACKGROUND INFORMATION
Remus and Sirius are married.
Voldemort raped Lily and got her pregnant.
Sirius and Remus adopted the child.
The Ministry of Magic cleared Sirius hours after the Potters' were murdered.
After James and Lily died, Sirius and Remus took in Harry.
Sirius disappeared when Calliope was five and Harry was three. He didn't return for nine years.
When Sirius disappeared, the Ministry claimed Remus had no legal guardianship over Harry and took him to Privet Drive.
Remus had the DADA position for two years before Sirius returned.
Time frame-Voldemort returned to power a year earlier than the books.
Same thing for the Order of the Pheonix.
Story takes place during Harry's 4th year in school
NOW ... ONTO THE STORY!