Here’s the solution:

Who is the murderer? How did it happen?

Yellow is the murderer. When Yellow bumped into Green in the hallway after the lights went out, Yellow took the hypospray that Green dropped in the collision. Yellow saw someone wearing the research lab access key card (which emitted a purple light in the darkness) and believed it was Dr. Blue who was intent on fulfilling their threat of dumping the cure. In the heat of the moment, Yellow used the hypospray to stab that person, who turned out to be Captain Black. Captain Black just moments ago violently grabbed the keycard from Dr. Blue, unbeknownst to the latter. Yellow expected to find the cure in the cabinet, now unlocked due to the power outage, but it was gone!

Where is the cure?

Where did it go? While Yellow was in the engine room figuring out how to power down the ship, Green was able to dump most of the cure using the access code and research lab access keycard that Dr. Blue had left for them in the cockpit. Indeed, these two were working together to destroy the unfinished cure, which took the life of Green’s twin and threatened the reputation of Dr. Blue. Green left one hypospray for safe keeping in Dr. Blue’s desk.

Who was the real engineer?

Neither Green nor Yellow were the real engineer assigned to the SS Karma. Yellow knocked out the real engineer on Sat 34, which later Green found. Green was truly a spacecraft engineer, but not the one assigned to SS Karma. Yellow is not an engineer, but rather, the inventor of android AIs which dominate every day life. Despite their vast wealth, Yellow was unable to purchase two doses of the cure for themselves and their child. Captain Black was resolute in implementing a fair lottery system for this batch of the cure.

What was the “truth” the Captain wanted to tell Red?

Red was indeed an android who had no knowledge of this beforehand. Red had recently began expressing emotions, almost all were positive due to the camaraderie between them and the Captain. The Captain believed it was time for Red to learn the truth. The Captain had always treated Red like a trusted friend, so Red had no reason to turn against his supposed “owner” like other sentient robots had. Red was, however, susceptible to the override code which Yellow, as the inventor of the androids, was of course familiar with. 

What happened in the cockpit when the lights turned off?

In the cockpit, just prior to the lights turning off, Captain Black and Dr. Blue were arguing fiercely. Captain Black grabbed Dr. Blue (to grab the access keycard), and when the lights turned off, the Captain immediately let go and exited the room while Red entered. Dr. Blue stabbed the hypospray into the darkness into Red’s neck, leaving a mark with traces of theorium. Being an android, Red woke up from their override state while Dr. Blue, believing they killed the Captain, hid in the security room. Red turned on the emergency landing sequence and went down the hall to resolve the power outage. Just as Red passed the research lab, the lights returned due to Green’s efforts, revealing a dead Captain Black.

What accounts for Red, Yellow, and Green’s missing memories and black outs?

Strangely, Green doesn’t remember leaving the security room, and Yellow doesn’t seem to recall giving the second command to Red. These were both indications of the short term amnesia that characterizes WRM-19. Timestamps of doors and other evidence, but not their memories, suggest that these things happened. Green blacked out for a few minutes after bumping into Yellow in the hallway after the lights were turned off. Red blacked out twice, once to open the security room cell door that let Green and Yellow out, and a second time to incapacitate the Captain and Dr. Blue when the lights turned off. The second command wasn’t performed due to the actions of Dr. Blue, who injected the android with theorium which results in the android waking up from the override state before one hour had elapsed.