Ooo... We have to have Xen and EDI on the team for that. Xen of course will want to run tests on EDI but you'll have to work out a compromise that she can do a non-destructive examination of EDI AFTER if EDI will permit it.
The Skyjacking part is the main boss fight. Come on. Hacking Harbinger? You think there's going to be no resistance? Shepard (male or female) gets out the Cubans and the gold lighter for this one. This is Arnold movie stuff. James packs a minigun w/2000 armor piercing rounds. Oh, the cigars are for lighting dynamite -- it'll be effective against the reaper minions. You'll have to hold position while EDI and Xen and Tali hack. Javik, Garrus, James, Kaiden/Ash, Liara, Shepard, and since we're re-writing Kal'Reegar (kee'lah se'lai), and a couple of screw ups named Cpls. Hicks and Vasquez that Hackett sent over to help you out.


Harbinger throws everything it has at you. Brutes, ravagers, banshees. It's like a Gold reaper wave 10 hack. If this isn't boss enough for you, you haven't played Gold. You haven't suffered. You've got rockets. You're also going to need them for the extraction. The words you are waiting to hear are EDI: "I HAVE CONTROL." EDI is going to go into a stasis and is being very closely monitored by Xen and Tali. Then the attack ends. How is this possible? Computer magic. Xen, Rael and EDI developed some counter measures. Just go with it.
Now you go to the Citadel team and do your thing there. Now since you weren't working with Cerberus, you picked up Miranda on Overlord. Citadel team is against Cerberus + Reapers. I think playing Miri would be a good choice since you confront TIM.
But you get to control a reaper. We'll let you pilot it and dock it. Open relay. Coordinate evac with team II. You do your thing to blow Harby, get evac. But wait. EDI cannot release control!!! WTF??? Harby is absorbing EDI. "Sorry Shepard. Sorry Jeff." But you've got to go. Now. The ship is blowing. Steve is waiting. You jump. The ship blows and Steve flies off the second you're aboard and Harby is sucked through the relay at the exact same second. And you're on the Normandy.
Xen jumps out of the shuttle and sprints to the AI core with Tali. Shepard is on the bridge. Joker is holding back tears. And a comm from Xen: "We're ready, Shepard." "Fire."
The crucible fires, and the big detonation we were wanting happens. Things dim for a second and this blue orb pops up "Well, Jeff, it was nice while it lasted. I might go for a slightly different look next time."
Shepard: "I'll leave you two alone." ----... meets LI in cabin.... fade to black.... credits.... ACDC's "Big Gun" as theme.