Both bcbdrums and GothicThundra have amazing fics with much angst around the aftermath of Drakken working with Warmonga. They're probably more fun to read, honestly (and you should), but here's a short about my HC anyway ...
–N
He left her to have a heart attack in the back of a police van. She abandoned him in prison. He ditched her to work with an alien and tied her up when she came back. She worked with their sworn enemy and foiled his near-success at world domination.
Drakken glared at Shego from across the table in their lair. Not the one he'd been in earlier this week, of course, since that one was a wreck. His wrist ached from where he'd sprained it escaping Warmonga, and his face was tattooed with fading bruises. Shego herself had a nasty cut on her cheek, and he knew by the way she moved that Warmonga had bruised Shego's ribs, at the very least.
"Even?" he asked.
Shego turned her eyes to the ceiling, considering it, and then said, "Yeah. Even."