IS WRONG!
I think I have figured out what happened regarding the whole timeline stuff. I'm amazed that there are no plot holes, I don't think that was pre planned but just dumb luck. Anyway context:
We all know that Cell came from a third timeline where Trunks was killed. So where did it all begin? Let's go
Timeline 1: Cyborgs, Goku virus, everyone dead Trunks travels back in time (Original)
Timeline 2: Trunks goes back in time, he warns the Z fighters, then comes back 3 years after they train to help them and they FAIL; cyborgs win again (I'll explain later). However chibi Trunks (We'll call him Trunks 2.0) grows up stronger for some reason, (perhaps Gohan 2.0 starts training him earlier) and this time Trunks 2.0 defeats the cyborgs (possibly with Gohan 2.0's help), at this point Trunks 2.0 still has the time machine that the dead Original Trunks from timeline 1 had and decides he's not done yet; he's going back in time for some reason Piccolo assumed in the manga that he was going back to tell them that he had defeated the cyborgs, (I'd like to think he was going back to gather the dragonballs and wish everything right) HOWEVER he is ambushed by Cell; Cell takes the time machine and goes back himself.
Timeline 3: Manga timeline; the events in timeline 2 where the Z fighters and Original Trunks die are interfered with by Cell so they never happen. (In a sense Cell saves their asses)
Timeline 4: in Timeline 1 Original Trunks never returned from Timeline 2 (pretty bleak timeline, I'm guessing Cell becomes perfect and wins there) but since Timeline 3 changed all that, a new timeline was created where Trunks returned to the future and killed the androids and the Cell of that time.
So Daizenshuu 7's theory about blueprint and remote controls was probably off the mark. What's not taken into account is that in the manga Cell came from a timeline where Future Trunks had killed Frieza because it is stated that Trunks's Cells could have been extracted. People assume however that since Cell came in a time machine where Trunks was planning to travel to the past then it was a timeline where Goku died from the virus. But it wasn't, we clearly see from the panels that Future Trunks had interfered with Cell's original timeline so the only conclusion is that even with Goku's help they fail to contain the cyborgs, I don't know what happens, but we must assume that at least the androids get them before they go into the room of spirit and time. Perhaps they start killing civilians and everyone is too distracted by that to think of going into the chamber. Or maybe 16 self destructs or something, whatever. Point is they die but the time machine is still around and chibi Trunks is still around and so the Trunks that Cell kills is the one belonging to that timeline, the one who eventually becomes strong enough to beat the androids but not quite strong enough to beat Cell.
What do you think? I suggest you catch up on the theories, I think I covered that plot hole pretty well
