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Tear Jerker: Star Trek: Enterprise
The alternate version of the 31th century seen in the "Shockwave" two-parter.
The real-world death of Kellie Waymire, who played recurring character and Love Interest of Phlox, Ensign Elizabeth Cutler. After her death in 2003 from an undiagnosed heart condition, the producers decided to quietly put her character on a bus and not re-cast her character out of respect.
The final scene of Season 2's "Cogenitor." The episode itself is arguably one of the most powerful Star Trek fans had seen in a long time, and the shockingly tragic Twist Ending ensures that status. (And it was written by the often-derided Berman and Braga, to boot!)
Travis learning of his father's death in "Horizon." Especially since the two never reconciled after Trav left the Horizon to join Starfleet.
Older Archer in "Twilight" learning that Enterprise's mission failed and Earth was destroyed.
The brief existence of Sim in "Similitude."
Malik's cold-blooded murder of his "siblings" Udar and Persis.
In an odd way, Silik's death was surprisingly tear-jerking.
The death of Admiral Forrest really came as a shock to many. It helps that he died saving Soval's life.
Trip's Story Arc in Season 3 as he attempts to ignore the death of his little sister during the Xindi attack, culminating in "The Forgotten" when he finally breaks down and admits to himself that Elizabeth is gone.
The last several minutes of "Zero Hour" when everyone thinks Archer is dead.
Trip and Hoshi dying in "Observer Effect." Even though they did get better.
The death of poor little baby Elizabeth makes the harsh comments that T'Les made about a human and Vulcan having a baby seem all the more Harsher in Hindsight.