Relationship(s) that may apply:
Harry Potter/Tom Riddle l Voldemort/Luna Lovegood
Harry Potter/Tom Riddle l Voldemort
Harry Potter/Luna Lovegood
Tom Riddle l Voldemort/Luna Lovegood
Luna and Harry are sort-of like forces of Light and Dark personified. A very rare occurrence.
These beings are not born with their full power, their bodies would be too fragile to handle the strain and also too emotional to keep it in check.
Lords of magic are capable of controlling these 'forces' to a certain extent, of guiding them so they stay in balance.
Anyone with enough magical awareness can feel the existence of these 'forces' -Lords of magic even more so- and most want to use them for their own personal gain. Magicals are also unnaturally drawn to these beings and even areas they frequent due to the magical residue left behind.
Dumbledore sees this as an opportunity to end Dark magic and the 'forces of evil' once and for all. (It could be that only Lords of Magic are capable of destroying -killing- their own affinities personified being, possibly as a natural safety precaution, in case one of these beings cannot handle their own power and cause unnecessary mayhem/destruction; this may also cause the Lord to die as well -it could be sacrificial magic). Dumbledore finds out that Harry is to be the next personification of Dark then fabricates a scenario (the prophecy) so Harry and Voldemort will die at the hands of each other or at least weaken Voldemort enough for Dumbledore to deal the final blow himself. Things do not go as planned.
For a complete AU: Voldemort would either not fall for Dumbledore's trap and not visit the Potters or take over the wizarding world completely, either way, he disregards the Potter boy as having any sort of 'vanquishing' power then odd years later and Harry is grown up (probably somewhere in his teens) it is discovered that Luna and Harry are not what they seem in some spectacular -and possibly public- manner.
Harry and Luna would try to hide what they are because they would be afraid of what people would want to do to them.
For something closer(?) to canon: Voldemort would go to the Potters, kill Harry's parents then get himself blown up, fast forward about a decade Voldemort would get his body back (probably by killing something or someone), start to gain his power base back by doing things (knocking on original followers doors, mingling at parties in different countries -he wants outside influence because most of the forces belonging to the dark have pretty much been demolished since his fall-, threatening people, etc.), and discover after some bullshit (Harry would try his damnedest to keep what he and Luna are a secret for as long as possible) that his enemy is not really his enemy.
Harry would be jaded as fuck because honestly fuck his home life with the muggles, I know what emotional abuse is like and that shit does not make you someone who sees the good in people and if I found out some old asshole got my parent's killed then sent me to a shit hole all because he discriminates against dark magic I would want to destroy him, so I imagine Harry working behind the scenes and possibly killing some people, mostly those on the light but some on the dark as well, who would not fit in a balanced world. He may be forced to work with Voldemort if he is unable to do something, plus he would have some sort of draw towards Voldemort.
It could be possible that if the magic isn't balanced it could affect the 'forces'. It could be that Luna may occasionally experience physical pain from the influx of magic but would try to keep it controlled to the best of her ability; she would often go to Harry for comfort if it gets to be too much.