I'll do my best to explain the time travel part of Only Death and Rage. Disclaimer : I do not own Phineas and Ferb

The whole time travel thing can be confusing so here it is. When you go back in time (or forward) you jump with the machine. Where ever the machine that's where you land in time. Your body is transported to where you need it so the fabric of time isn't messed up to bad.

I'm going to be making the murder scene that Ferb is in, as a prequel. So hang on while I write that.

It will be written in Ferb's perspective. Even while he's in heaven.