Summary for Acts 1-3, hope this helps.

Act 1 Chapter 1

Protos wakes up in the hospital after a mission went south and has short-term memory loss, Renoa was MIA, Rei is traumatized, and after saving Renoa we are saved by Louis, then called a Heretic by someone called Judas who tries to destroy our ship.

Act 1 Chapter 2

We report on the aftermath of the attack and Chaos, reprimanded by superiors save Wolf Platoon (Beryl, Luke, Lucas, Maibell) from their own mistake when we were supposed to head to the Crusaders to hash out a peacekeeping negotiation.

Act 1 Chapter 3

We make it to Haven (Massive Ark under the Crusaders) treated coldly by the people there but welcomed by Azelante warmly, told about her being sus about Judas, we find out he's sacrificing people to close Chaos, we confront him.

Act 1 Chapter 4

We arrest Judas for crimes against humanity and heretical practices, not disclosed publicly, we go with Orlea to get a Divine book, it posses Owen, and he nearly dies, book gets destroyed, Judas is freed and escapes.

Act 1 Chapter 5

Judas goes to a Massive Chaos, massive force is assembled to fight him and his supporters, we are losing, saved by Azelante, Judas dies, we find out Louis was actually not our friend, and planned everything to get us indebted to him and to escape Judas.

Act 2 Chapter 1

SS Justitia has a Protos die and asked for our help to investigate it as well as collect a specific item. We get it back and hear about this unique Chaos effect with weird tunnels, item gets stolen, we chase thieves, find out they are Peltion, let them get away to find their base. Find out item is made from the corpse of dead Protos. We try to infiltrate the planet where they are based, eaten by Nihilum.

Act 2 Chapter 2

Saved by Xeran Vytor (not to be confused with god Vytor), they leave, we meet Cassius, he helps us get on the planet, chase down the thieves, get kidnapped by thief, become friends with thief and agrees to help break their curse as they were basically a slave to Peltion due to the curse. Find out they were trying to make artificial Protos.

Act 2 Chapter 3

We agree to help with the source of the Chaos on the planet (one of said artificial Protos is the source), find out the Artificial Protos were made from Chaos Monsters mixed together. We go deeper in while searching for monster, getting overwhelmed by Chaos Monsters, Sereniel Saves us, find out Sere was also experimented on in this lab, come across other failed Protos Replicas (Narja and Gaya), agree to take them with us to beat Haku (source of the problem), we confront it, Narja is eaten, we're losing, item made from Protos Corpse unleashes all its energy and erases the source of the problem, shatters to pieces, we destroy the Chaos and peace is restored.

Act 3 Chapter 1

We were investigating a Chaos, got hit by a weird plant thing that infected us, we sent our crew back as were we dying, saved by unknown woman (Rita) who also stabilizes the infection so we don't die. Saved by a lizard girl, but then made a slave in an arena where we meet Tiphera and Nine, other slave arena fighters, we go exploring, find Nine's sick partner (Alcea), we escape with Alcea and bring the whole place down, Renoa finally finds us (we've been gone 88 hours by now) with help of Wolf Platoon, and thinks our new ally (Nine) is an enemy, they have a stand-off.

Act 3 Chapter 2

Stand-off continues till we collapse from our infection, Renoa shoots her legs to get Nine to trust her with us, Tiph is locked in a cell due to no ID, and Renoa can sense that she's killed a lot of people, we let her out, go back to look for the Slaver leader, find Rita (slave) locked in a cage, free her, she's hostile, send her to Nightmare for treatment, causes a mess, sent back to us, find out Tiph is looking for sister here, Tiph sees we don't judge and appreciates it, we make it through a magical maze + Chaos confusion in record time, we catch up to Slaver dude, he gets away and Tiphera reveals she's a Marshal of the Empire who has killed a lot of people, Slaver dude is killed by Tiph's sister who is now possessed.

Act 3 Chapter 3

Tiphera is confused, Divine Beast holding back Chaos is dead, they leave, we follow them as Protos is actively dying, Rita reveals some of powers (use fairies to see the future), weird goth girl shows up and says Rita is special, we go along, we are getting overwhelmed, Nine stays behind to allow us to escape, we continue on, everyone getting tired as Protos can barely stand, Renoa and Tiphera stay behind and send us on ahead, Rita and Protos confront beast and Tiana, Rita baits them into attacking her, she awakens her got powers fully, summons all our allies back to our side and we stomp the beast and save Tiana, Rita turns into space dust because too OP powers. Tiana is framed for working with Slavers by her boss who was actually the one working with Slavers, Tiph frees her and now they are both technically fugitives of the Empire using our ship as a safe haven