You should, if all goes well, be able to win. I'd look for a defense drone, I'd upgrade shields to at least 3 bubbles (I know you have the Zoltan shield, that helps, but still, for the flagship you're going to want more shields), and I'd maybe swap out a beam for a pew-pew if you can find a decent one. Or upgrade your hacking. That works too. And sell some stuff. I'd sell both the system repair and the anti-drone, but that's just because I find the anti-drone downright useless. Sell one of your missiles, probably the breach, and sell a beam, you absolutely don't need 3 of them. With that cash you can buy some upgrades, I would prioritize hacking and oxygen. A helm upgrade also wouldn't hurt, but only do that if you have the cash for it, I wouldn't make it a priority!
System repair is good to have if you already have drones. The helm upgrade actually should have been priority #1! It's not for the effect but the damage buffer. If helm is at level 2 your evasion doesn't immediately go to zero when helm takes 1 damage. The compound effect of piloting being knocked out can be absolutely devastating and I'd suggest it as the very first thing you spend scrap on. Strictly because it let's helm take an extra hit before being totally disabled. The same applies to a few systems though I'd make it less a priority. A level 2 med bay or o2 room doesn't ever need to be powered to level 2, but the empty power slot ensures the system will run after a hit, I'd especially consider doing this for weapons and if you have dome extra scrap near end game and are okay working with 3 shields, that power slot that doesn't amount to a full shield still means you keep your shield at full even if it's hit once instead of losing layer if one laser shot gets through.
You should, if all goes well, be able to win. I'd look for a defense drone, I'd upgrade shields to at least 3 bubbles (I know you have the Zoltan shield, that helps, but still, for the flagship you're going to want more shields), and I'd maybe swap out a beam for a pew-pew if you can find a decent one. Or upgrade your hacking. That works too. And sell some stuff. I'd sell both the system repair and the anti-drone, but that's just because I find the anti-drone downright useless. Sell one of your missiles, probably the breach, and sell a beam, you absolutely don't need 3 of them. With that cash you can buy some upgrades, I would prioritize hacking and oxygen. A helm upgrade also wouldn't hurt, but only do that if you have the cash for it, I wouldn't make it a priority!
System repair is good to have if you already have drones. The helm upgrade actually should have been priority #1! It's not for the effect but the damage buffer. If helm is at level 2 your evasion doesn't immediately go to zero when helm takes 1 damage. The compound effect of piloting being knocked out can be absolutely devastating and I'd suggest it as the very first thing you spend scrap on. Strictly because it let's helm take an extra hit before being totally disabled. The same applies to a few systems though I'd make it less a priority. A level 2 med bay or o2 room doesn't ever need to be powered to level 2, but the empty power slot ensures the system will run after a hit, I'd especially consider doing this for weapons and if you have dome extra scrap near end game and are okay working with 3 shields, that power slot that doesn't amount to a full shield still means you keep your shield at full even if it's hit once instead of losing layer if one laser shot gets through.