Timeline:
Begins: Summer after 5th year.
Ending: Unknown.

Alterations to Canon:
Potentially. In canon only Teddy provides any data on when metamorphmagi develop their talent, whether or not all metamorphmagi do so at or immediately after birth is unknown.

Pairings:
Harry/Tonks

Story:
When Harry is sent by Petunia to get milk from the nearest convenience store he overhears taunting voices chanting 'Freak! Freak! Freak!' coming from around the back of the store. Going around the building to take a peek he finds several kids, about 10 years old, gathered around someone curled up on the ground.

Thinking for a moment he walks back to the side alley and lifts the lid on one of the rubbish bins and loudly slams it before shouting: 'Who's there? What do you think you are doing?' In predictable fashion the bullies have scarpered before Harry has returned to the back of the store.

Approaching the figure on the ground he discovers she is a girl, also about 10 and paradoxically wearing a ski-cap at the height of summer. When he reaches down to help her up he gets a surprise when he is lightly blasted (by what can only be accidental magic) into the back wall of the store and has the wind knocked out of him. The girl, seeing what just happened, freaks out and runs... but stops at the end of the alleyway.

Realising that he must have been the one to scare the bullies away she decides to go back and, standing well away, quietly asks Harry if he's okay. Reassuring her that he is fine he stops when he spots that a lock of her hair, sticking out from under her ski-cap, is changing colour from red to green as he watches. Immediately the young girl figures out what he's looking at and starts backing away again.

Harry however, mind racing, talks her down and just asks if they were bullying her because of her hair. In response to her anxious silence he lifts his fringe to show her his scar and tells her that because of it bullies used to pick on him, in fact he was once chased behind this same store and beat up too.

Samantha (or, whatever name you choose) cautiously allows Harry to lead her home, a home she snuck out of because her parents have had her basically under house-arrest since her hair started changing three months ago. When they arrive Sam's mother is home (her father is out looking for her) and engulfs Sam in a hug, stiffly thanking Harry for Sam's safe return before she quickly dismisses him and locks the door in his face - over Sam's loud protest that Harry is nice.

Only the abrupt dismissal manages to prevent Harry from blurting out what he suspects is the truth. While walking home he begins to reflect that it was probably for the best considering that he'd have no means of proving magic existed to them while he's still subject to the Trace and that it's probably against the Statute to tell them until Sam is eleven. When he arrives back at Privet Drive he doesn't see (but hears and smells) Dung's presence snoring away under the bushes and suddenly Harry realises that there's someone who would be perfect for the job of breaking the news to Sam's family.

A couple of days later while listening carefully and circling around the block he hears his minder stumble, fall and colourfully curse. Backtracking to help Tonks up off the ground he tells her that he has something he needs to show her and leads her to Sam's house.

Sam's Dad is not at all amused to meet him when he opens the door to find Harry and darkly states he'll call the police if he doesn't leave immediately. Harry just asks if Sam is there. Moments later, over her mother's shout to stop, Sam thunders down the stairs, her shifting-rainbow coloured hair flying behind her as she grins up at Harry, glad he came to visit. Harry greets Sam and tells her that he's brought someone very special to meet her.

At this point Sam's parents are terrified, this is exactly what they were afraid would happen. Their panic is instantly interrupted when Tonks, standing next to Harry, pulls her invisibility cloak off and reveals herself. Sam is startled but her eyes grow huge as they watch Tonks' hair shift colour, just like hers.

Later that evening two very relieved but no less shocked and confounded parents see Harry and Tonks off after they learn their daughter is a witch and a metamorphmagus as well. Tonks is no less moved from her encounter, having never met another full-metamorph like herself (most metamorphs are limited to only minor or superficial changes to one or two characteristic of their body) and sincerely thanks Harry for introducing her to Sam.

Over the remainder of the summer every day that Tonks is on 'Harry Watch' they go over to Sam's house. Partly it's to help fill Sam's parents in on the magical world and to expect a letter on Sam's 11th birthday in three month's time (just missing Hogwarts' next term), as well as to help Sam start getting a grasp on controlling her morphing but mostly the days are about livening up Sam's life and having fun now that she doesn't have to be locked up alone.

The time Harry and Tonks spend together begins to change their relationship and feelings between the two develop but aren't acted on. The summer continues with Tonks and Harry interacting when he is at the Burrow, while visiting Diagon Alley and then when Tonks rescues Harry from the Express after his run-in with Draco. At this point Harry shares his suspicions, based on what he overheard and what he witnessed that Draco is Marked and has a mission from the Dark Lord inside of Hogwarts.

Fast Forward:
Dumbledore dismisses Tonks' concerns - knowing the truth thanks to Snape - frustrating the Auror considerably who is worried for Harry, considering he'll no doubt try to stop Draco and could get hurt in the process. Dumbledore's decision is taken out of his hands though when Katie Bell is cursed by the Necklace on her Hogsmeade trip and the DMLE gets wind of it. Scrimgeour unequivocably states that if the children of Wizarding Britain are under threat from the Dark then he must act to protect them and Dumbledore complies, seeing several Aurors stationed on the grounds and Tonks assigned undercover.

She assumes a new identity and is 're-sorted' into Hufflepuff under the guise of a former home-school student whose parents felt she would be safer from Death Eaters at Hogwarts for her sixth year. Under her new identity she 'infiltrates' Harry's circle of friends (Hermione, Ron, Ginny, Luna and Neville) and begins assisting Harry to investigate and then when she learns the utter lacking of actual training in Dumbledore's 'private lessons' she takes on the job of instructing Harry with her combat knowledge as an Auror.

Inevitably the time spent together with Tonks morphed to the same physical age as Harry removes a lot of the barriers that had held Tonks and Harry back from acting or speaking on their growing feelings towards each other and eventually they capitulate, giving in to their emotions and urges resulting in a secret relationship.

What Next?:
Harry becomes a badass 'super-Auror' or something? Is it a partnership effort of just Tonks and Harry or does he bring in the 'Ministry Six'? Or the whole DA to train in preparation?

Do they foil Draco's efforts with the Vanishing Cabinet or not? Do Harry or Tonks tell the others who she really is? Or do the others discover some other way? Before or after Harry and Tonks have started a relationship? How does it affect the outcome of the year or the Horcrux hunt to follow?

Harry and Tonks should keep up correspondence with Sam throughout the year and eventually I would hope she'd be brought back into the story if only to warn her not to go to Hogwarts for her first year in 1997 if the story follows canon insofar as Dumbledore's death and Snape/Carrows taking over the school.