An alcoholic, abusive British (just to please Yahtzee ^_^) Sergeant serving in Afghanistan suddenly wakes up at 4AM in the morning with a blinding ache - his entire body is screaming in pain. Seconds later, he hears explosions and gunshots as alarm bells go off - fourteen militants have broken into the camp. He runs outside, but unable to find a gun or ammunition, is chased by the militants. Gameplay starts here, as Sergeant Tommy Paxton experiences three simultaneous seizures. In a cutscene, he is set on fire, frozen in ice and zapped with a million volts of electricity. He wakes to find the fourteen militants standing around him, and begins to fight them.
Not with guns, but with either fire, water/ice or electricity.
It turns out he's a Sapient (okay, shameless self-incorporation there), a supernatural being, one of those who have existed since the beginning of time, always living in secret. The combat style is unique - you have standard attacks, but use x button to switch between fire, ice and electricity. You can imbue your weapons with this, but only logically - obviously, setting a grenade on fire is going to blow you to hell, so you could use it to turn it into an ice shard grenade.
After the fight versus the three militants, you are kidnapped from Afghanistan two days later and wake up in London, with the head Sapient next to your bed. He makes you an offer to join the exoSkeleton, a group of surviving Sapient fighting against bounty hunters, the supernatural and governments. You have the choice of whether or whether not to join them, and the story goes on in nonlinearity.
The Sapient is a sandbox style procedure - whether or whether not you accept the head's offer, you will gain the Sapientsoul. This allows you to customize your power, going from the power of the elements to psychic, dark powers, or powers to generally fuck with the laws of nature, or the laws of physics. The game will incorporate minor time travel - you can use your power to go backwards in time ten seconds to headshot that pesky enemy that took out half your health ten seconds after (confusing, but bear with me). Either way, your power is completely customizable, and there is a good/evil system. However, whether you burn pregnant mothers or travel to Tanzania and provide power for the citizens, it will have an effect on gameplay, not story, therefore allowing you to sandbox in a huge open environment without having to fear that the story will get worse.
This is a very rough draft, btw.