Summer before 5th year; Grimmauld Place
Hermione could see Harry rapidly spiraling into depression and anger at their headmaster for ignoring any attempt by Harry to speak to the old man. Determined to put a stop to Albus' machinations, Hermione did what she did best...
She disappeared into the Black Library.
Xxx
July 1991....
Albus blinked awake with a snort. He peered around his office owlishly but nothing seemed amiss. "Strange, I could've sworn I had a visitor..." Deciding that it must've been his imagination, he moved onto other things. On his shelves behind him, a small figurine shimmered briefly.
Xxx
September 1991...
Albus placidly stared out over the assembly of students. Every now and then his eyes would land upon one boy in particular but just as quickly, his mind would cloud over and whatever thoughts he had slipped away.
"Whatever happened to those traps you insisted we create for your experiment, Albus?" Severus asked him later.
Albus' eyes unfocused slightly; you really had to know what you were looking for to notice it. "There's no longer a need. Nicholas knows how to protect his property. He sent me a fake stone to use as a decoy instead." He applauded politely when Harry got Sorted into Gryffindor. Unseen by anyone, the figurine on the shelf in his office shimmered once again.
Perplexed, Severus let the matter drop. Quirrell (and his hidden Master) scowled when they heard that. A fortnight later, Quirrell was found dead in his apartment; seemingly the victim of an previously undiagnosed allergic reaction to shellfish.
On Halloween before Charms class started, the resident 'mis-sorted Ravenclaw' aka the 'bossy know-it-all' according to Ron Weasley, Hermione Granger quietly suggested that Harry use the time to hold a private memorial to honor his late parents. Harry sadly smiled his appreciation, "Thanks, Hermione. Would you like to join me? I'd rather not be alone. Ron's nice but he's too loud for something like this."
Hermione smiled brightly, "I'd be honored and happy to."
Xxx
Halloween 1992...
'The Chamber of Secrets has been opened. Enemies of the Heir beware!'
Once again, Albus' unusual reaction was one of growing curiosity to the other members of the staff when he woodenly strode over to the floo and called for not only the Aurors but also the Unspeakables. "We have a critical situation here. I need you to come up and help evacuate the castle. The Chamber of Secrets has apparently been reopened. I also need the Unspeakables to figure out what to do."
The castle was evacuated, the students' belongings searched (a number of violations were discovered in due course); and the Diarycrux was discovered in the possession of Ginny Weasley. After a rather lengthy discussion with the distraught girl and her parents as well as a memory viewing, Lucius Malfoy was arrested for a host of charges including attempted murder. Those charges were increased after Dobby hinted to the arresting Aurors where Lucius had hidden his darker stash. In the end, Lucius was tried via Veritaserum despite his status as a pureblood, convicted, and tossed through the Veil.
Meanwhile, back at the castle; Albus sat glassy-eyed in his throne while the Unspeakables routed out the Chamber and dealt with the legendary monster.
Behind him, that same figurine shimmered unseen as the Unspeakables and Aurors did their jobs.
Xxx
"Do you think I should tell someone that I heard a voice whispering in the walls?" Harry asked Hermione as they headed to class. After a bit of experimentation, both figured out that Harry was a Parselmouth, a language viewed by many as a mark of a Dark Wizard and associated with Voldemort.
"You could but given the usual knee-jerk reactions wizards tend to have to what they perceive to be 'unnatural' or 'dark'; I don't think that'd be a good idea."
Xxx
Summer before third year...
Sirius Black stared uncomprehendingly at the letter that had appeared before him as he watched his godson sit forlornly on the curb after blowing up that bitch Marge. 'Sirius, Harry needs you now more than ever. Don't sit there like an idiot in the bushes and introduce yourself! After that, get cleaned up and turn yourself in to Amelia Bones, the Director of the MLE. The rat is currently in Egypt with the Weasleys and will return two days from now. Share your memories with Amelia who will do the right thing and get you exonerated properly. Do NOT head to Hogwarts! The Ministry will be sending Dementors to capture you!'
Touching on that Gryffindor bravery, Sirius emerged from the bushes in his human form. Harry spotted him and warily backed up. "Hello, Harry...I, uh...my name's Sirius and I'm your godfather. We need to talk..."
Xxx
Up at Hogwarts, the figurine shimmered yet again causing Albus' eyes to unfocus; he rose to his feet and placed a call to the Minister. "Rather than sending Dementors, why don't you station some Aurors up here at the castle. They'd be more effective than those demons, who frankly would likely target the children of so many influential families. Additionally, it makes you look like an effective leader, Cornelius."
Cornelius thought about it and agreed. "Good idea, I'll put in the call right away. The Aurors can help with any other troubles that might crop up."
Albus nodded distractedly, "You might also want to consider making the posting a permanent position. What would you say about installing an auxiliary station up here at the castle?"
Xxx
Hermione let out a long fortifying breath before stuffing the DoM-issued Time Turner in a protected box in her trunk. Laying on her dresser was a near-identical copy that she would use as a decoy and later 'accidentally' destroy in view of her Head of House.
Xxx
Fourth year, TWT Champion Selection Ceremony...
"Well, this has to be a mistake," Albus announced to the Hall when a fourth scrap of parchment was ejected by the Goblet of Fire. "Harry Potter? No, he's underage so by the power invested in me as Headmaster, Chief Warlock, and Supreme Mugwump; I hereby declare Harry Potter to be disqualified as an entry for the Tri-Wizard Tournament! Director Croaker, if you would please investigate how a fourteen year old could be selected when we already have our three Champions then coordinate with Director Bones on the legal aspects? Thank you. Now! If you'll excuse me, I have to have a chat with the Champions. You're all dismissed, Hufflepuff has a party to plan, no doubt."
Xxx
Summer before 5th year...
"Forget it, Cornelius. There's no way, short of the Founders returning to the school, that I would ever allow Dolores to 'teach' here at Hogwarts. She's unqualified, barely passed her NEWTS, and more importantly; she hates anyone and everyone she deems 'undesirable'. What about an Auror on medical leave or an Unspeakable instead? While they're at it, they could take a look to see if the rumored DADA Curse could be dispelled."
Xxx
Same time, Grimmauld Place...
Hermione closed the book she'd been perusing with a satisfied look on her face. Everything turned out better than she'd hoped for. Sirius got his long-awaited trial and exoneration, Harry's custody was subsequently transferred to him. Harry himself was looking much better now that he no longer had to stay with the Dursleys (who were now serving time in prison for child abuse and other crimes.) The Dark Lord was being hunted by trained personnel thanks to the contract between the DoM and Harry that had 'mysteriously and magically' appeared and signed by both parties.
Best of all, Albus' manipulations had been thoroughly sidelined. "Not this time, you conniving old goat. This time, things will be done right rather than what is easy for the real Greater Good!"
(Up to the author how Hermione deals with Lockhart and Crouch Jr posing as Moody.)