Biomimetic lifeforms' homecoming
A story that was under consideration by the writing staff of Star Trek: Voyager involved "Silver Blood" duplicates of the USS Voyager's crew, biomimetic lifeforms that would ultimately appear in the episodes "Demon" and "Course: Oblivion". The undeveloped plot would have featured the duplicates being welcomed "back" to the Alpha Quadrant. (Star Trek: Action!, p. 5; Cinefantastique, Vol. 31, No. 11, p. 49) Jeri Taylor explained, "Everybody thinks that Voyager is home and there are celebrations, and they see their loved ones, etcetera, etcetera. And it turns out to be an invasion or a dark plot of some kind." (Star Trek: Action!, p. 5) Joe Menosky elaborated, "Brannon [Braga] had some great images. One was opening with Voyager above Earth, this great homecoming sequence. There are fireworks in the sky, and everybody is going down to their homecomings. Janeway has a wonderful tearful reunion with Mark. She kisses Mark and she then snaps his neck, end of teaser. Then he had this image of like a thousand Voyagers converging on Earth. Somehow, these duplicate Voyagers were being created that didn't even know who they were." (Cinefantastique, Vol. 31, No. 11, p. 49) According to Jeri Taylor, another of the plot ideas was that the duplicates would arrive, amid great fanfare, at Deep Space 9. (Star Trek: Action!, p. 5)
The story was devised at the end of Voyager's third season. "Writing the teleplay, it just didn't seem to work," said Joe Menosky. "We shelved it, and did 'Scorpion' [and 'Scorpion, Part II'] instead." During the fourth season, the shelved plot was repeatedly reconsidered, as a possible two-parter, but was replaced first by "Year of Hell" and "Year of Hell, Part II", and then (months later) by "The Killing Game" and "The Killing Game, Part II". (Cinefantastique, Vol. 31, No. 11, p. 49) It was also considered as a potentially usable but unlikely fourth season finale, towards the end of that season (specifically, shortly before and on 2 February 1998, just prior to the writing of the actual fourth season finale, "Hope and Fear"). (Star Trek: Action!, p. 5) Joe Menosky commented, "The mimetic aliens got to have this really weird reputation as being a negative muse. It was this weird thing that no one wanted in the room." (Cinefantastique, Vol. 31, No. 11, p. 49) At about the end of the fourth season, Jeri Taylor offered, "The more we discussed it, the more we thought that once they go home, even if it isn't really our characters, well, it undercuts whatever will happen when the real crew actually does get home. Which we do intend to have happen." (Star Trek: Action!, p. 6) Regarding the fact that the alien duplicates of the discarded narrative ultimately turned up in "Demon" and "Course: Oblivion", Joe Menosky concluded, "Ironically, the mimetic alien show became a two-parter in a strange way." (Cinefantastique, Vol. 31, No. 11, p. 49)
Jamahl Epsicokhan pitches
In 2000, Star Trek: Voyager reviewer Jamahl Epsicokhan was invited to pitch stories for the series. On the third of October he traveled to Los Angeles and pitched four stories to Bryan Fuller, all of which were rejected.
This story would have seen Voyager mediate a dispute between an asteroid base on a critical mission of mining a substance used in battling a epidemic, and a rogue planet steered into the system by it's inhabitants to escape a supernova. The insertion of the planet in its new orbit would wipe out the asteroid belt and thus the base. 
A story focusing on Seven of Nine, which after an accident lost 75% of her Borg nanoprobes. This would have left her more Human, for example she was not able to regenerate anymore and thus had to learn to sleep. However, while Janeway welcomed this opportunity, Seven herself set her sight on a medical procedure that would restart nanoprobe production. The story was rejected by Fuller because it was too similar to a seventh season story in broken just a week earlier, in which Seven's Borg regulator failed and and one of the Borg children, Icheb, wanted to donate a piece of technology to save her. (presumably "Imperfection") 
This story would see Voyager lending assistance to a planet suffering the ill-effects of a recent wormhole-creation experiment gone awry. They also met an alien, which maintained that any help from Voyager would cause more disaster. Ultimatly the alien would try to stop Voyager himself, causing an event that sent him back in time with only the memory that Voyager must be stopped, a paradox. The story was rejected as too complex, and the alien's motivations similar to captain Braxton's in "Future's End" 
Do No Harm
This story would have the Doctor being forced to kill someone to protect another crew member while on a medical mission of mercy on a war-torn planet. This contradiction of his Hippocratic Oath programing would have left the doctor disturbed, and he would work through his issues by talking about violence with fellow crewmembers like former Maquis-members Chakotay and B'Elanna, and by visiting a number of violent holodeck programs. The story was rejected as being too similar to "Latent Image", and Fuller's opinion that the Doctor would not be so naive concerning death and violence.
Q on a beach
A Q story for Star Trek: Voyager was pitched by Q actor John de Lancie. Supervising Producer Joe Menosky explained, "Brannon [Braga] and I went to Rick Berman's house for Thanksgiving dinner, and Brent Spiner and John de Lancie were there [....] John had an idea for a Q episode. He had a couple of interesting images, of Q on an ocean somewhere on a beach, either having lost his complete identity as Q, or lost his will to live. Somehow he gets involved with an everyday kind of person, and that person's fate and life somehow affects Q. That was his pitch, and it had some nice images." (Cinefantastique, Vol. 31, No. 11, p. 51) This not developed story idea influentially sparked the writing of the fifth season Voyager episode "11:59". The story is similar to some elements in de Lancie's later novel, I, Q.
The terminator drone
In the process that ultimately lead to him writing "Drone", Harry "Doc" Kloor pitched several other stories. The filmed episode evolved from a very different pitch, called "The Terminator drone". It involved Seven of Nine's nanoprobes infecting the holo-emmiter, creating a killer drone. This was further modified and became "Drone". 
Tom Paris story
In the process that ultimately lead to him writing "Drone", Harry "Doc" Kloor pitched several others. His first idea had Tom Paris crashing on an alien planet, his arm almost completely ripped off. A character from an advanced race present on the planet then re-attaches the arm with Borg technology. The idea was rejected as too gory. 
Visit to a Small Planet
About two years before the release of Galaxy Quest, Jack Treviño and Toni Marberry pitched this story where the crew came upon a planet that had been observing their lives on Voyager for the last three years, and where everyone was dressed as members of the crew. As such, the crew are forced to see themselves through alien eyes. The writers felt that the fans would not accept the show having fun at their expense.  In some elements, this premise is similar to "Muse", "Blink of an Eye" and "Virtuoso".
Janeway on trial
"When we were talking story before the season began, I thought, 'One of the shows you should do is the trial of Captain Janeway. You should have the crew, one day, put her on trial.' That would be a real major thing in life of the ship, if the crew can do that, if they really have the power to take command away from her at any moment. If they are really willing to put her under that kind of microscope, it calls into question the entire structure of the show, the entire social fabric, the command structure. Why are we behaving in this way? Why do we hew to these rules anymore? Do the rules still apply to us? What do we find within the rules that work? What do we find that doesn't work? What does it say about Janeway? I thought that there is ground to play there. Nobody wants to go there. On the one hand, you hear them say, 'We don't want the Captain to look weak.' They don't want to make Janeway look foolish. But then the things that you do make her look weak and foolish anyway. It's this strange, schizophrenic attitude about their lead character. I like Kate Mulgrew. I found her a charming, funny, very personable woman sitting on the set next to her. I think if they could let her do more of her own thing in the character, not straight jacket her so much, it would be a more interesting dynamic."