In Cell's original timeline, an alternate Future Trunks went into the past and helped Goku just as in the main timeline. Future Trunks and the Z Fighters manage to defeat the Androids and he travels back to his alternate future timeline. Since this was a completely different timeline, the events of Cell never occurred and he did not expect to encounter Cell (and may not have even been aware of Cell's existence). When he returned to Age 788 of his alternate future timeline, he disabled the other future Androids and was going to go back to the past to tell the others of their defeat. Instead, he ran into and fought with Cell who killed him and then went on to take Future Trunks' time machine into the main timeline. The death of Future Trunks seemingly brought the Saiyan race to extinction in his specific timeline. Cell was then killed in the main timeline by Gohan. However, the time machine this Future Trunks used became really useful for the primary timeline Future Trunks in Super - after his own time machine was destroyed by Black, Bulma revealed to Future Trunks that she had kept the alternate time machine stowed away for her own studies.
This alternate Future Trunks is mentioned by the primary Future Trunks in the PSP game Dragon Ball Z: Shin Budokai where, upon meeting Cell, Future Trunks mentions that he will redeem his alternate counterpart for failing to stop Cell.
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