Starting journey 3 - am I screwed? (Spoilers)

At the end of Act 2 - which I managed to pull off with only 1 day to spare - the technician and 2 other alters knocked me out and left the mission.

Like…do I keep going or do I need to restart? I’m not sure how I can succeed with the loss of three of them including the guy who maintains the base? Or do I press on and it’s solvable?