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The Zoltan and their ships are really particular in that it’s less power hungry than other ship, due to the fact that the Zoltan provide a free energy power and that the Zoltan Shield allow to redirect the normal shield power to other system. The Zoltan energy can be use to remove energy from recharging system like cloaking, boarding system, hacking and mind control simply by walking in and out of the room. Because of this it make the main reactor less a priority than usual and you can focus more on buying a system upgrade versus extra power in the main reactor.  It can be good idea to upgrade a system evens if it cannot be powered continuously. This gives you more room to juggle power distribution and meet particular demands. Another tactic that you can do with the Zoltan is to use them has bomb when boarding with a clone bay (see Layout C of the Federation Cruiser for more details on that technique).

Another side note once you get a non Zoltan crew member, move him or her into the pilot’s chair so your former pilot’s Zoltan energy can power one of the systems. Zoltan energy don’t power up sub-system like doors, piloting, camera and backup battery.

Layout A:

Zoltan Cruiser

Unlock

Complete the Unarmed Zoltan Transport random event.
Or defeat The Rebel Flagship with the Federation Cruiser.

This ship has one of my favorite weapon, the Halberd Beam will cut through most ship you encounter in the first few sector and it will still be useful even late game. This Weapon usually stay the whole game. Beam weapon can be somewhat tricky but if you maximize the number of rooms it you can take out most of the early ship in one beam. Remember this beam deal 2 dmg so even against 1 shield enemy you can still use it but it will only do 1 dmg instead of 2. Once you start encountering enemies with two or more shield levels, you may want to use missiles to take out their shields or use an ion weapon. It is best to time your beam shots precisely when the enemy shield is hit, rather than putting your beam weapon on auto-fire.

This ship could really use the Weapons Pre-Igniter giving you the ability to take down most ship without your Zoltan Shield going down.

 Layout B:

Zoltan Cruiser

Unlock

Earning two of the three Zoltan Cruiser achievements will unlock Layout B.

The Noether (Zoltan Cruiser Layout B) starts with only one bar of power in the shield system, requiring 100 scrap to upgrade once and get to Level 1 Shields.

The Noether (Zoltan Cruiser - layout B)

You have to rely on your Zoltan shield until you upgrade the shield for 100 scrap, speed is your friend here so you need to quickly disable the shield to be able to blast the enemies ship with the Pike Beam. Like the previous layout the Weapons Pre-Igniter can be a nice addition and later be useful when you get even better weapon. Cloaking is a nice addition too since it give your Zoltan shield extra time. Without shield asteroid field will be a problem, you might want to avoid those. Another other issue with the Zoltan in general is their lack of hp, which make them venerable to boarding (except if you have a clone bay).

Layout C:

Zoltan Cruiser

Unlock

Getting to Sector 8 with the The Zoltan Cruiser Type B with Advanced Edition Content enabled will unlock Layout C.

Starts with two bars of reactor power, requiring 30 scrap to upgrading the first 3 points.

The reactor is super low but 4 Zoltan and a level 2 Backup Battery should cover your need pretty early on. The starting combo of this ship is to use the Ion Charger to disable shields and then activate your drone with the backup battery.

Side note: the lack of need for the reactor of this ship makes Ion storms, weapons and pulsar little threat and even help you against enemies.