Seriously flawed… Janeway must have gone off her meds…
This is the 6th season opener of the "cliff-hanging" ending to the 5th season. In Part I, Voyager encounters another ship in the Delta Quadrant. It's a science ship called the Equinox with a smaller crew and is led by Captain Ransom. This ship is under attack by an alien life form from another dimension. It turns out in Part I, that Ransom and his crew were capturing the aliens and then using their dead bodies as fuel to get home. An act that Janeway considers illegal. She imprisons the Equinox crew but they manage to escape back to the Equinox where they take off leaving Voyager at the mercy of the attacking aliens. So ends Season 5. Generally, an exciting episode. The story picks up in Season 6 with an immediate tonal change. Janeway immediately begins acting irrationally and out of character. Rather than dealing with the aliens attacking Voyager, she decides to go after Ransom and the Equinox. She captures one of the crew and demands to know Ransom's status. He refuses to comply so she removes the shielding around the cargo bay so the aliens will attack and kill him. She's convinced he will "break" before that happens. Chakotay steps in before that happens and for this act, she removes him from command.
Compounding things, when she finally acquiesces to Chakotay and Tuvok wanting to talk to the aliens, she promises the aliens she will turn the Equinox and its crew over to them.
Ultimately, this becomes a story trying to create and play out a theme. There's two starship captains, one (Ransom) has crossed the line and wants to go back. His first officer, (Burke) resists and won't let that happen. Janeway is also crossing lines and her first officer (Chakotay) resists it. The Doctors (both the EMH on Voyager as well on the Equinox) can have their ethical sub-routines turned off with a single switch. I suspect that's supposed to be saying something about humans (Ransom and Janeway) flipping their ethics on and off with relative easy.
First of all, I really don't buy it since we've spent six years with Janeway and although she's proven unstable and belligerent at times, she's never been this far out of whack. Secondly, this is very damaging to her character with little in the way of payback. A lot of the adventure as well as tension in the episode could have been handled without her going to these extremes.
The final scene involves Voyager's name plate which has fallen off the wall. (In Part I, the Equinox plate also fell off the wall). Janeway and Chakotay are going to put it back, no doubt symbolizing a return to the higher standards being on Voyager demands. I'm not too sure the ending shouldn't have been Chakotay locking Janeway in the brig. Or, the now ethically inclined Doctor could have given her a shot and explained away her bizarre behavior as a result her earlier direct encounter with the alien life form.