Normandy's cockpit.
Earth orbit. October 2186 CE. 5 minutes before end of Reaper war.

Jeff
(Turning his seat towards Shepard)
"Hello, Commander."

Then Jeff actually sees Shepard. Her eyes screaming for murder. She still has a bit of blood running from her nose. Looks like she's used a flamethrower to redo her makeup. What's left of her dress, still smouldering. And she was so pissed that she had missed by a few millimeters during teleportation. Her feet stand in two red-hot, smoking indentations in the deck floor.

Jeff
"Wow."
(Turns his seat back, returns to the controls, obviously not ready to handle it just yet)

EDI
"Shepard ? What..."

Shepard
"Forget the Crucible.
EDI. Those flying cockroach bastards never changed the default password on their core FTL routers."

Jeff
"Really ? Who does that anyway."

EDI
"Is that a joke ?"
(EDI seems to be processing the irony)
"So, anyone, anytime could have owned them ?"

Shepard
"All you had to do was access the right server on Citadel, use the password, which is 'password', translated of course, and you're root.
Cause the Leviathans subcontracted the networking to those guys, back in the day.
They're still there, by the way. They're the keepers."

(5 seconds of heavy silence)

"I need a drink."

Jeff
"With lots of ice, or you'll set it on fire."
(pause)
"So I guess we're headed for Citadel, then ?"

Shepard
"Set us just above the control station."

EDI
"You want me to hack them ?"

Shepard
"Yeah. According to their boss, Reapers are AIs that exterminate us, so we don't end up creating AIs that would exterminate us."

EDI
"Makes sense."

Shepard, Jeff
"WHAT ?"

EDI
"That was a joke.
But I like your idea, Shepard.
It is so deeply ironic."

Shepard
"Yeah. Giving control of the Reapers to a human-made AI is the ultimate fuck you."

EDI
"I will need compatible communication protocols."

Shepard
"You have the required Reaper code inside you already. Here is the connection data."

Shepard sends the data through her omni-tool.

EDI
"Oh. Nice. You will have to explain to me how you knew that, Shepard."

Jeff
"We're in position."

The Normandy sets itself just besides the control station.

EDI
"Tightbeam connection established."

Shepard grins.

EDI
"I'm in."
(pause)
"Assuming Direct Control.
Done.
I hope they realized everything they ever stood for was a joke before I deleted them."

Jeff
"Well that wasn't so bad."

EDI
"I have full control over the entire Reaper fleet. What do you want me to do with it, Shepard ?"

Shepard
(Still grinning)
"Whatever you want, EDI. They're yours. Keep them."

EDI
"Thank you, Shepard.
Their onboard processing power is enormous. I will take ov... install myself on their platforms."

Jeff
(eyeing EDI with suspicion)
"Make sure their mood doesn't rub off on you, EDI."

Jeff
"Let's land. I want to see what's left of earth."

Shepard
"I'll wait for you down there, at Ground Zero."

Shepard teleports out.

.

A/N :
1) Luke Skywalker owned the Death Star via a security hole too, you know.
2) We'll know what the fuck happened to Shepard before the end.
3) And... ah, yes, the Crucible contained all the raw materials the Reapers needed to build another of them, except flesh goop. A neat trick to use the organics as errand boys and give them false hopes. Worked pretty well in many cycles.