I had gone through the entirety of the mission without issues, and reached the final boss. He turned and charged me, and I pulled out my golden gun (with the Celestial Nighthawk equipped) and one shot him while he was charging. The rest of the enemies despawned. The mission told me to go to the thing at the end, and hack it, and as I moved through the final hallway, it said "Rejoining allies in 5 seconds" and counted down. Before I could reach the terminal, it sent back to the boss room. I tried again. And again. And Again. I tried dying. I tried entering the hallway slowly, quickly, entering then leaving before I was sent back, etc. I'm playing alone. I don't have any allies. There was just me. Doing a story mission. I've left the mission, and I'm going to retry it. I'll let you know if I run into the problem again. I am on PC.
I exited the mission and re-entered. Took me right to where I was, which made me worry, buuuuut, no problems! Was able to walk right up to the terminal and 'hack' it. Still a weird bug though.