Basket takes the Stealth Cruiser back out "to see if we can do better this time." The ship is The Nesasio on Normal with Advanced Edition content enabled: no shields, a Cloaking system, a Mini Beam and Dual Lasers, and the Long-Ranged Scanners and Titanium System Casing augmentations. The crew list shows three Humans, Shelton, Elnubnub and Chriz. Over six parts the crew grows to seven, and The Nesasio destroys the Rebel Flagship in Sector 8 with three of them still aboard.
Part 1: A free Ion Blast
Sector 1 is a Civilian Sector. The plan is the same as last run: wait for the enemy to fire, then cloak. After the first fight, against a Pirate Scout, a fourth crew member, Maria, joins the crew list. A Rebel Rigger hacks the ship and still loses its weapons.
At one beacon Basket tells a nearby station about the flight from the Rebels, and the station hands over an Ion Blast Mark II. "So this thing charges very quickly... man, that's awesome." Basket also puts scrap into the cloak again: "Last time we played the cloaking one, we had a three cloak, and that was really nice."
Sector 2 is Rock Controlled. A Rock Scout goes down and a later ship surrenders for fuel ("we need some more fuel to get to this area"). A store offers Drone Control and Shields, but there is not enough scrap for either.
Part 2: Mantis space
Sector 3 is a Mantis Controlled Sector. A Mantis Scout is overheard planning to put a prisoner "out of the airlock," and Basket attacks it. Later a young Mantis teleports aboard begging for sanctuary from the Engi, and Basket sides with the fugitive. The Engi Bomber that follows has "a lot of weapons" and hurts the ship before the fight is won. "This is working, but it was very painful."
A slave trader, a Pirate Light-Cruiser, is attacked rather than paid. It surrenders and offers a crew member: "Yes, I would like your guy, thank you." Borman joins. A Rebel Disruptor surrenders too, and Basket spends scrap on the cloak once more. At the exit a refugee convoy asks for help, and Basket declines.
Part 3: Three shields and a near miss
Sector 4 is Rebel Controlled. At the first store Basket sells the Backup DNA Bank for repairs and fuel. Then an Auto-Assault with three shields fights back hard. Fires spread, the oxygen fails, and the hull bar drops into "Hull Critical." The cloak and the Mini Beam finally take its weapons down. "Thank God we survived that."
Sector 5 is Rebel Controlled again. A distress call from a burning research station ends with a Zoltan Shield Bypass on board. Scrap piles up to 249. "We're pretty decked out... We just have to find a store."
Part 4: The Zoltan quest
Basket picks Sector 6, the Zoltan Homeworlds, hoping for a quest. A store finally has what Basket wants. The ship gets Shields and a Defense Drone Mark II, and Basket sells the Zoltan Shield Bypass and upgrades the reactor.
The quest leads to a Rebel Rigger. Basket hails it instead of attacking, and picks the peaceful answers: "Let's be super peaceful, guys." A Zoltan fleet appears, the Zoltan captain joins as Envoy, and the event text reads "A Zoltan cruiser has been unlocked and added to the hangar!" "We've unlocked another ship," Basket says.
Part 5: A Vulcan for the end
Sector 7 is the Rock Homeworlds. A Rock Fighter with four shields is beaten anyway, and at the next store Basket buys a Vulcan. "This is going to be our main weapon. Hopefully that's a good choice." The Ion Blast goes into cargo.
A life form on a moon turns out to be Charlie, a seventh crew member. A Rock war vessel offers a quest, but the event text says there is no time: "You leave the quest for another day." A Small Bomb comes free at the next beacon, an automated ship with a hacking system is beaten, and the part ends at the exit to the last sector.
Part 6: The Last Stand
Sector 8 is The Last Stand. An Elite Fighter at the fleet's beacon hurts the ship on the way to the Federation base. Then comes the Rebel Flagship.
The first stage goes well. Basket says it did not take much damage. In the second stage drones swarm the ship, the crew list loses Shelton, and Basket asks, "We no longer have a captain, so who's gonna be captain?" The third stage is the hardest. Boarders teleport in, Maria gets mind-controlled, fires spread and crew members fall. The hull drops to its last point. "And this is probably when we die right here," Basket says, but the cloak comes back up and the Flagship goes down.
How it ended
The end crawl thanks "The Nesasio" and "her successful crew: Maria, Envoy and Charlie." The victory screen reads "Congratulations! You've defeated the Rebel Flagship and ensured the victory of the Federation!" with a score of 3425. "I had one health," Basket says. The ship best list now shows The Nesasio at 3425, Sector 8, Victory. Basket then looks at the newly unlocked Zoltan Cruiser in the hangar before the end cards.