I was in a Shadowrun as a player where my GM setup that EXACT idea.
We started as what we thought was the "good guys", being led astray by a Mr Johnson and an evil corp. Then later, we started another game that we didn't know was about the same thing.
After a while, both parties encountered each other. We started a fight, then the GM pulled our old sheet and asked us to control both sides.
The fight was an absolute mess of metagaming, everyone using ALL they knew about both sides to make decisions that, while strategic and smart, were so metagaming it wasn't even funny.
"hey the shaman doesn't have healing but can incapacitate us all with this. TAKE HIM OUT FIRST"
We finished the fight, where basically the side who won was the side we "wanted" to win (cause we made sure they had the upper hand). We then all looked at each other, admitted how crappy this was from an RP perspective.
The GM apologized, and we agreed to retcon the encounter. The GM changed the abilities of the party a bit (to be less predictable/reflect the time they spent getting better since WE last saw them), and we redid it, with the GM controlling the other party.
Don't try. It makes for a good narrative. But if you make the players control both sides, it's just a bad experience in the fight itself. I mean... try playing chess against yourself. It's.... not great :/ (to my taste at least).
If you are hellbent on doing this... involve your players from the getgo so they KNOW this is about to happen.