Here is an app that tries to make plotting out your story very easy: Plottr
It's got a timeline that is a very graphical way to show each story line (main plot and subplots) and each scene. Across the top are the scenes and along the side are the story lines. You aren't held to specific dates on the timeline. It let's you put in whatever description you want across the top.
The nice thing is that you can flip it so the scenes are down the side and the story lines are across the top. It's better for some people to see it like that.
Where the scene and story line intersect you can add a card which is just a place you can write a description about what happens at the intersection of those two.
You can even drag and drop cards easily anywhere around the timeline.
It also has a place for general notes, a place for characters, and a place for settings. For characters and settings you can add custom attributes which is really handy.
And the notes you can tag with your characters or places.
I use it for my stories and it's been invaluable