Episode 30. After spending 13 years and all the series trying to save their families, the episode has our heroes forced to sacrifice their loved ones to foil the Big Bad. Made even worse when the team leave hyperspace, and each of the original trio try to deal with their pain in a different way.
Episode 50. Jin pulls a Heroic Sacrifice to destroy Card no. 13, freeing Hiromu and ending Enter's immortality. His speech beforehand, the reactions of the heroes to his plan and his and Hiromu's father's data remnants telling them to return home after Enter's defeat only adds to it all. Sayonara, Beet Buster...
And he appears and waves to Kuroki back at the base before fading away.
In Go-Busters vs. Gokaiger, the Buddyroids have to use some of their own Enetron to transport everyone back to the present from where they were trapped in the past. This, combined with taking damage during the transport, causes serious damage to their programs, and when they're finally repaired they no longer have their personalities. The Busters... don't take it well. And then later they actually have to go into battle with Go-Buster Oh this way.
But due to The Power of Friendship, the core three Buddyroids get better, the Go-Busters are overjoyed, and the Gōkaigers unlock the Greater Power of the Go-Busters, their bond with their True Companions, the Buddyroids.