Don't know where to begin?

While ultimately it doesn't matter which arc you begin with, Cecil arc is recommended if you want my recommendation.

And then Masu arc + Shattered union arc. 

Feel free to visit the lore section as well which holds stories of its own.

Legends arc (4)

This arc covers stories that don't deserve its own arc.

It's often legends and historical events. There is no time limit or main character in this arc.

[Legends arc] [Andromeda rebellion] [9071]

This is the story about Andromeda rebellion occurred on 9077 and their success, thus forming Andromeda republic.

This story commended to be read AFTER when you finish the six stories in Cecil arc. However, this is a standalone story and may be read without having read any of Two Clusters stories.

Additionally, this is a fairly long story.

[Legends arc] [Freedom colony] [8489]

There are not many stories that center around Lila (Lilicious) but she does appear in a fair amount of stories as a side character and whatnot. She is an important character but just doesn’t have the presence to have her own arc.

This story is about her; how she started out and so on. And this is one of very few stories that cover Aedy Freedom.

Because this story recalls events in the past, it will have quite a bit of related stories. They MUST be read prior reading this.

[Legends arc] [Venus] [2799]

An ancient story regarding attempts to terraform Venus.

[Legends arc][Magnificent end][9889]

This is where Lila (AKA Lilicious) story ends. She may still appear in other arcs in earlier years, but this story includes her life.