The End of Trinity ending appeared in Part 2 of Sally.exe Continued Nightmare: Eye of Three when Cream was killed by the mind-controlled Amy during Sally's fight with her. It was removed in the update.
After Amy fades away after the fight, Sally laments that she lost and asks the girls to forgive her, but states that she can't say the same for herself. She walks off-screen afterwards.
Sally appears at Fatal Iron, where she sees a laser overhead and is scared. She successfully walks ahead, but then she is affected by the "Eye". After the laser shoots again, she walks under it and closes her eyes as she waits for it to fire, killing herself.