To watch all of The Star Trek franchise, it would take you nearly a month of no-sleep-marathoning. Nearly 550 hours at this point. Twenty-four days. AND THEY'RE STILL MAKING MORE. You don't have that kind of time.
I've attempted to put together a much more condensed series of Star Trek. Dividing it into ten episode seasons. For the most part, these are My Favorite Episodes. I've left out some that are historically important episodes, in favor of things that I found fun to watch. If you're a Trekkie or Trekker, or just consider yourself a fan, I may have left off your favorite episode. Sorry. But this is more a list for people like me, who had seen an episode here and there, were interested in seeing more, but don't want to invest in the whole 530+ hours. I'm doing it, so others don't have to.
With the ending of TNG, we are left with two atypical Star Trek series: Deep Space Nine, which takes place mostly on a space station near a wormhole, and Voyager, which is your typical federation starship, but lost on the opposite side of space from the federation, and made up of a crew that is half federation, and half Maquis terrorist. These are both brilliant conceptual twists on Star Trek. Sadly, Voyager never delivers on its potential. I'm not saying that it's terrible, I'm saying that the Maquis/federation angle is never fleshed out as well as the space station angle of Deep Space Nine.
This season focuses on the show Deep Space Nine, but focuses on episodes that mostly revolve around one of their ships, The Defiant, which is the first cloakable federation vessel. The Defiant gets much use as the federation gets embroiled in a constantly shifting war this season, which introduces new villainous aliens, and upgrades some old school aliens to new adversarial heights.
Episode 1: Jem'Hadar
(Sisko, Jake, Quark, Nog, Odo, Kira, Dax, O'Brien, Bashir)
A father/son bonding trip between Sisko and Jake (as well as Quark and his nephew Nog) goes horribly awry when they are kidnapped by the new Big Bad of Deep Space Nine. Forget the Cardassians, the Jem'Hadar are nonfuckwithable warriors from the other side of the wormhole, and they're about to change the whole feel of the series.
Episode 2: The Search
(Sisko, Odo, Quark, Kira, Bashir, Dax, O'Brien, Garak)
So, it turns out the Jem'Hadar are just soldiers who work for The Founders, and they are the unfuckwithable adversaries for the season. Starfleet uses their newest ship, The Defiant, to try and track them down. But the Jem'Hadar have other plans. Oh, and Odo ends up finally meeting aliens just like him.
Episode 3: Improbable Cause/Die Is Cast
(Garak,Odo, Bashir, Sisko, O'Brien, Dax, Kira, Eddington)
It has been inferred since the beginning of Deep Space Nine, that Garak, a Cardassian tailor, is actually a high ranking spy. So when his shop is blown up under mysterious circumstances, Bashir and Odo delve into his past.
Episode 4: The Adversary
(Sisko, Dax, O'Brien, Eddington, Jake, Quark, Kira, Odo, Bashir)
Like Odo, The Founders are all changelings, so imagine the damage they could do if they infiltrated Starfleet and Deep Space Nine. Oh, shit, did that already happen?
Episode 5: Maneuvers
(Janeway, Chakotay, Torres, Kim, Seska, Tuvok, Neelix, Paris)
The closest Voyager comes to making the Maquis/federation conflict work is the character Seska, a Cardassian who was living as a Bajoran. She defects from Voyager before this episode and joins up with the Kazon, who are The Big Bads of the first three seasons of Voyager, but who pale in comparison to The Klingons, The Romulans, The Cardassians The Borg, The Jem'Hadar, The Founders, the spooky children of The Original Series, Tribbles, evil Kirk from the Mirror Universe, a stick of gum that gets caught in your sneaker treads. They're a lame adversary, and they're rarely a threat. Until they get combines with Seska. This also sets up a storyarc that will be in the 5 Bonus Episodes at the end of this post. But this is, by far, the best of the Seska episodes.
Episode 6: Way Of The Warrior
(Worf, Sisko, Odo, Kira, Dax, Garak, O'Brien, Gowran, Quark, Gul Dukat, Bashir)
The Klingons haven't been a big part of Deep Space Nine. Sure, Dax and some of her Klingon friends went on an adventure, and yea, the sisters of Duras were around for an early episode, but for the most part, they haven't been very present. But when Gowran decides The Klingon Empire should protect the wormhole from The Founders, he incites a war between The Klingons and The Cardassians, and it gets so intense that Deep Space Nine recruits Worf from Enterprise to join their crew.
Episode 7: Homefront
(Sisko, Odo, Jake, Nog)
What if The Founders reached Earth, which has been a paradise since the beginning of this series (apart from the whole Borg attack in Best Of Both Worlds a few seasons ago, and the whale problem from The Voyage Home)? Sisko, Odo, and Jake return to San Francisco (say that five times fast) to help prepare the planet, only to discover The Founders may already be there. This is a particularly good episode about fear mongering and the loss of freedom due to the fear of terrorism (and this was a pre 9/11 series). It's technically part one of a two-part arc, but the second half undoes the power of this episode, if it existed in a vacuum.
Episode 8: To The Death
(Sisko, Worf, Dax, Bashir, Kira, Odo, Quark)
After Deep Space Nine is attacked by a faction of the Jem'Hadar, the crew of The Defiant run into another faction of Jem'Hadar who were also attacked. The two crews work together to take down the first faction. There are some great moments of culture examination in this episode between The Jem'Hadar, humans, Klingons, and The Founders. Deep Space Nine was truly the best Star Trek series when it comes to examining how every side in a war is actually The Bad Side.
Episode 9: Broken Link
(Odo, Sisko, Worf, Dax, Garak, O'Brien, Bashir, Kira, Quark, Gowran)
When Odo falls ill, the crew of Deep Space Nine must take a ship other than The Defiant to The Dominion in hopes that The Founders will help him get better.
Episode 10: Apocalypse Rising
(Sisko, Odo, Worf, Kira, Bashir, O'Brien, Gul Dukat, Gowran, Quark, Dax, Jake)
At the beginning of the season, it seemed like The Jem'Hadar were the all powerful enemies, but it turned out that they just serve The Founders. Then the Klingons got involved. Then we went to Earth and it looked like maybe The Founders had taken over Starfleet. But what if they actually took over the Klingons? They are Everywhere. And Sisko, Odo, O'Brien, and Worf have to go undercover to unmask Gowran (who, apart from Worf, has the longest ongoing storyline this season). And Sisko makes A Fantastic Klingon. It's a joy to watch.
Five bonus episodes, if you like this season:
The Defiant is not a great episode. But it does feature Riker, sort of, and it's a somewhat interesting diversion from the heaviness of this season. It would go after "The Search" in this continuity. After "Maneuvers", I would check out Hippocratic Oath, where Bashir and O'Brien have to help some Jem'Hadar who are trying to break their addiction to the drug that The Founders use to keep them loyal. I would follow that up with Meld, which is a Voyager episode that shows the danger of the Vulcan mind meld when, in order to solve the motive of a murder, Tuvok melds with a sociopathic Betazoid. It almost made the actual list for this season, but like many Voyager episodes, the ending where they dumbed it all down in conversation annoyed me enough to wish I hadn't been so invested in it. After "Homefront, there's a Voyager episode called The Basics that ties together the fallout from "Meld" and "Maneuvers" in a mostly satisfying way. If it tied things up a little less neatly, the whole storyarc might have been the crux of this season. If you are willing to endure some sloppy writing and terrible acting in order to get a glimpse of the TNG and TOS casts this season, I would follow up "The Basics" with Generations where, at the very least, you get to see Kirk and Picard interact for the only time, and say goodbye to Scott and Chekov.