I think the way to go would be to draw inspiration from the current Indestructible Hulk series. Basically, Banner gets a platform for scientific research, and in exchange, SHIELD gets to aim and deploy Hulk as a (rather unconventional) weapon.
I especially like the concept of a Bruce Banner-based software floating around, guiding and trying to keep Hulk under control. I would even go so far as to project Banner's head, Jor-El style from a tiny floating droid, thus giving Ruffalo more screen time. I'm thinking Hulk destroys this contraption a few times before begrudgingly accepting his punier self as his play caller.
0-15 min: Open with Hulk in mid-air, dropped head first onto a tiny island, possibly the MCU equivalent of AIM Island. Hulk goes ballistic, obliterating pretty much everything.
15-45 min: We rewind things a bit and see how we got there... Banner approaches Maria Hill with an ultimatum, albeit one he pitches as mutually beneficial. We get to meet his supporting staff: something similar but not a direct copy of the current Agents of SHIELD crew. Some back and forth with a typically combative and exasperated Maria Hill, etc. Hill goes over AIM and/or Evil Organization X's latest world dominating/obliterating shenanigans, the first mission plan, etc. They're in a plane above the island when Hill pushes Banner out of the plane. To add insult to the uninjurable [sic], she shoots him in the head as the highly anticipated first transformation occurs mid-air.
45-108 min: Back to the aftermath of the first successful mission, and... ah, screw it. This stuff writes itself. What do you want from me?