This is the basic breakdown of the plot of RFI, using Dan Harmon's Story Circle.
¶ You (Establish a Protagonist)
Miranda Collins, a young military officer, receives an imtimidating new assignment.
Miranda Collins is the new Ops Officer of the Archigos. She is just transferring aboard and meets some of the other crew members. We feel sympathy for her because she's the only new transfer onboard the ship, the ship had to go out of it's way to get her, and she's feeling awkward in a new place.
¶ Need (Something Ain't Quite Right)
Miranda discovers the pending Terran attack on Tel'Erani.
Miranda is checking sensor readings from Tel'Erani, and notices what appears to be three ships making their way towards the system. She is able to show that they're Terran warships, and they plan on invading the system.
¶ Go (Crossing the Threshold)
A Sooni murders the captain and most of the bridge crew, with only Miranda surviving.
While preparing for the Terran attack, a Sooni assassin murders the captain and most of the bridge crew, with Miranda only surviving because of Glyse. Now, Miranda is the acting Captain, and must hold the line long enough to report back about the mysterious assassin.
¶ Search (The Road of Trials)
Miranda ends up sacrificing the ship the save the colony.
Tel'Erani,it turns out, is a Freelance colony world giving aid to Lyndri refugees. There are millions of people on the planet, and very few ships. There's no way they can evacuate and no way they can even aid in their defense.
To defend the colony, Miranda leads the Archigos into a pitched battle, but the ship keeps taking damage. They do their best, but ultimately, Miranda decides to sacrifice the ship (and possibly her crew) to save the colony.
¶ Find (The Meeting with the Goddess)
Miranda meets with Admiral McKenzie, who explains what's really going on.
Miranda survives Tel'Erani, and is offered a promotion to Captain of the [Rekonin][]. However, that promotion comes with the cost of knowledge, if she accepts it, she gets to learn what's really going on and the war that is really being fought. She says yes, and the whole situation with the Sooni, Focus, etc. is explained.
¶ Take (Meet your Maker)
The human governments collapse and Miranda faces off against Sean's forces. They only win once Daniels sacrifices himself.
The Sooni kill off the leaders of the human governments. Chaos ensues and Sean and his forces start invading. Rekonin tries to fight them off, and gets it's ass handed to it. Daniels sacrifices himself, allowing them to get their first win against Sean's forces.
However, in retaliation, Sean has decided to blow up earth.
¶ Return (Bringing it Home)
Miranda regroups with McKenzie and makes a plan to save Earth.
Rekonin returns home and Miranda and McKenzie, and they gather their forces and make their assault plan.
¶ Change (Master of Both Worlds)
Miranda and Rekonin fight against Sean and with the help of their new forces, win.
Miranda's forces enter the system, and the convince the Terrans they're there to help. The battle starts, and it's not going great. Then, the Lyndri show up in their ancient dreadnaughts here to help because of Miranda's sacrifices at Tel'Erani. With them come the NorAellians and Emelyn, leading a fleet of Freelance ships. Miranda has the forces she needs because of her actions in Tel'Erani.
She defeats Sean, and they can finally contemplate rebuilding the galaxy with a unified human government.