To polish this idea, the first thing I'd suggest is double checking your grammar and spelling. There are a couple of rough places in your descriptions where the sentences seem kind of jumbled, in addition to the usual typos.

As I understand it thus far, your magic system could be summed up like this: [list]
[*]Rare humans are born with the ability to perceive and manipulate Mana. In addition to being able to sense Mana, a structure within them called the Mana Valve determines how much Mana they can use at a given time.
[*]Channeling Mana through the Mana Valve and into one's movements allows them to trace Runes in the air. Runes act as instructions to create the user's desired effect out of Mana, like a piece of code that tells a computer to display a "Hello World!" message.
[*]Mana itself is present as a non-tangible property within both organic and inorganic matter, within living things and inanimate objects. Only magic users can draw it out of the environment and into their Mana Valve.[/list]

If all that is correct, then my suggestion to create a plot would be to further elaborate, whether privately or with your Players, on the logical conclusions of this system. [@ArcticWasHere]'s suggestion that "Maybe Mana itself is depleting for some reason?" is a good one. If you want more conflict, then the cause of the Mana Depletion doesn't have to be "natural." It COULD be natural--maybe the Earth goes through phases where Mana depletes and replenishes like it goes through hothouse-ages and ice-ages in terms of climate. The conflict could come from the idea that Magical Society has become so reliant on heavy Mana usage--the way we're reliant on fossil fuels--that this period of depletion is going to cause massive resource shortages or cause some kind of important spellcraft or magi-tech to fail (like say, a barrier that keeps the Non-Magical Humans out). 

OR, maybe the Mana Depletion is being caused by a power-hungry magician who's created a Weapon of Mass Destruction--his machine, or ritual array, whatever, is absorbing a huge amount of Mana for some nefarious purpose. Maybe he wants to magically nuke Europe and usher in an age of wizard supremacy.

You could also generate ideas for plots by asking yourself questions like: [list]
[*]What Subjects are taught at this Magic School? Easy ones would be things like "Magical History," "Elemental Manipulation," or "Familiar Contracts." There could be more specialized subjects or extra-curriculars, though, like "Wizard Duels" or "Dragon Riding" that you could have Players compete in, either with each other or other magical schools.
[*]Are Runes standardized across all magic-users, or can individuals create their own "coded" Runes? Are all previously existing spells recorded in textbooks and libraries, or does each magic user come up with their own personalized methods of casting?
[*]How does technology interact with magic? Can Runes be carved or painted onto objects to permanently imbue them with magic?
[*]If the magic users are capable of great power, what reasons are there for them to hide from modern society? Are they simply outnumbered? Does a magician's most powerful combat spell still pale in comparison to a .50 BMG? Is an invisibility spell thwarted by thermal scanners?[/list]

I could probably sit here and ask more questions all day long, but you don't need to know every little minutia about your setting at this point. The point is that by asking these questions, you create reasons for organizations, factions, ambitious individuals, etc to exist. Maybe a government Black Ops program wants to force magic users to become super soldiers, or they've created Artificial Mages of their own who infiltrate the Magic School as spies. Maybe a powerful seal on an ancient demon beneath the school is getting weaker, and it's exerting its influence to create a cult within the school. So on and so forth.

I hope this helps, and wish you luck with the idea!