@DobbyTheHouseElk
The M15 Botox woman was so distracting I don’t know what she said, why use an actor with a face that doesn’t move.
Maybe she's just meant to be expressionless.
I think the plot has become clearer
The main thing is the Russians trying to reduce the West's nuclear capabilities by undermining public support for submarine borne weapons, and causing major disruption to the fleet.
They are doing this by trying to bring down a submarine.
Port Haven was initiated by them - much off the crew off board and drunk/high anyhow. Others spiked, including the guy who was transferred (drugged to sleep), everything left nicely cooking and the perpetrator off the boat. Nuclear disaster in a US naval port with Brits to blame, also blowing the transatlantic defence relationship out of the water (all evidence of Russian involvement destroyed when it went up)
Plot foiled because beardy heroin bloke returned sober.
Burke, the protesters et al see some of what has been wrong on the submarine, but don't know the bigger plot. Burke has been making records of everything that is wrong on the boat - many of which will be red herrings. Because there's probably always stuff like affairs going on. Others will be acting out of misplaced) sense of what is right (such as doctor with urine tests, or XO demonising Burke) and that muddies the waters.
The Russians are continuing the plot, because they have the assets in place to sabotage, even if not by a spectacular in a US base. They are however increasingly worried about people who are finding out bits of the preparations, and need to act occasionally to prevent discovery.
They have an asset amongst the protestors (bad on MI5 for not finding that) - probably someone Jade confided in (the politician could be in the frame for that - recruited by the Russians, telling them what he's heard from Jade without realising any of the significance, just hoping to get rid of the bases from Scotland). Burke collected the info for it to be used, OK it was found in his shore quarters, but Jade knew the password and so may have seen some/all of it.
The Russians wanted Burke out of the way, as something they were aware he had found out was getting too close.
But they might have needed to send a message to their on-board assassin to tell him/her to act, which they did opportunistically during disruption to routine following Burke's outburst. Message could be in pre-arranged language an innocuous family message, just as the detectives communicate. Precise timing of his death didn't matter, just as long as it happened.
The cook was vulnerable to exploitation because of her son, so may have been the poisoner. She may in turn have been poisoned, or may have chosen suicide, as the enormity of what she has done and a belief that the net is closing around her begins to dawn on her.
But even though submarine crew often multi-role, she is unlikely to have had the skill set to sabotage a submarine (given how highly qualified and trained the crew is). So is there another on-board asset Russian co-optee as well? And if so, are they committed to a suicide mission (seems possible, given the reactor fault)