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Left: "Scorpion" Part 2 trailer. Right: Fan created musical montage from "Fury."
Janeway forges an alliance with the Borg for safe passage through their space. In return they will help them develop a weapon to use against Species 8472. When the Captain insists on a representative to communicate with, they are assigned Seven of Nine. There's a scary scene with Kes in sickbay. She's working on something and sees a reflection of a member of Species 8472 coming towards her, she turns to see nothing there. Then when she turns around again, it's headed for her and she screams! Then the Doctor finds her safe. Kes's telepathic contact with Species 8472 continues and she helps on the Bridge. A perfect conclusion to my favourite two-parter, I still get as excited as when I first saw it.
Seven of Nine begins the transition from Borg
drone to an individual and member of the crew. We bid farewell to
Kes. Kes's mental abilities rapidly increase. FIrst a medical
instrument she needs flies into her hand. When Seven becomes
unstable due to her Borg implants, Kes sees insi
de her body with her mind and destroys
the implant causing trouble. Later, when Seven attempts to
contact the Borg collective, Kes causes a power overload to stop
her. But the crew discover Kes is damaging the structure of the
ship. Neelix opens a bottle of Talaxian champagne as he says they
did when they first came aboard and toast to the voyage ahead.
Kes's abilites become unmanageable and she decides to leave
Voyager. There's an emotional goodbye with Janeway. They head to
the shuttlebay when Kes can't control what's happening to her.
Tuvok performs a mind-meld to give her more strength to make it
(the transporters won't work). Kes appears to ascends to a higher
plane of existance and her gift to the crew is to push Voyager
10,000 light years (10 years) closer to home and past Borg space.
It's all very rushed and a bit silly, i.e. her powers are out of control and she has to leave! But it's handled very well, emotionally. She gets final scenes with Neelix, Janeway, Tuvok, The Doctor and Tom Paris looks sad when he hears the news she's leaving. But the others don't mention it, did Chakotay, B'Elanna and Harry not care? I guess she had no relationship with them over the three years. Janeway's teary goodbye was authentic, on the DVD special features Kate Mulgrew said no acting was required; she was upset to have Jennifer leave.
A much older and more powerful Kes returns to
Voyager in an attempt to change her history. Kes crashes her ship
into Voyager and causes lots of damage. Her mental abilities have
definately evolved when we see her throw the security officers
out of the way with the power of her mind. She goes to
Engineering, drawing power from the warp core to travel back in
time, to a period during the first season, and kills B'Elanna
when she tries to stop her. It turns out that Kes blamed Captain
Janeway for corrupting her younger self and wants to change
history by going back to Ocampa and delivering Voyager into the
hands of the Vidiians. 
Things are made harder by Neelix being
so loving towards her! It comes to a showdown between Janeway and
Kes, the Captain being forced to fire on Kes. She gets the Kes
from that period to record a message to her future self to
prevent the same from happening again. When history repeats
itself older Kes remembers who she was and how loved she was.
I remember how excited I was to see this episode for the first time. Jennifer is amazing playing a deceptive and evil Kes. I know many Kes fans were disappointed she came back this way but I love it. An older Kes may well have changed a great deal, in the Ocampa lifespan it's the equivilant of 25 years later. The storyline has its flaws though. Once older Kes sees the message her younger self made everything's fine and she says "these years were full of such confusion." But the older Kes has become bitter and regrets her decisions so it kind of makes sense but I can't help feel the character's reasoning for doing all of this wasn't very good. If all we could have was one episode of Kes, it makes sense she'd be deeply troubled, helped to overcome this by the crew and heads off again though. It's action packed, an imposter on board in the past and a return for the scary Vidiians. At the end, when the older Kes doesn't know what to do, Janeway says "stay here with us," and I'm like "yes, please please please!" It's a thoughtful touch that it's "Also Starring Jennifer Lien" instead of "Guest Starring."
References: There are only three mentions of Kes in the forth season. Neelix says that he hasn't been with anyone since Kes when he's interested in someone and isn't sure how to go about it in "Random Thoughts." He uses a flower from Kes's garden for his vision quest in the fantastic "Mortal Coil". The Doctor is doing social excercises with Seven of Nine (his new pupil, kind of) in one episode, and says he used to do them with Kes. She isn't mentioned at all in the fifth season. In the sixth, Seven thinks Kes's departure was a way of Janeway silencing her about a conspiracy in "The Voyager Conspiracy." Then came "Fury." Again in Season 7 there was not even a Kes reference. The Ocampa and the Caretaker are occasionally mentioned when explaining how the crew were stranded.