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High-end equipment for the Skunk available through crafting items dropped as loot:

1. Mk5 engines
2. Mk3 Particle RepeaterMk3 Particle Repeater 
3. SETA
4. Jumpdrive

High-end shields for the Skunk are available through crafting rare items (details here):

1. Mk5 shields
2. Mk5 shields (second chance to purchase them)*

Crafting

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All related items can be found and crafted at any time, but in order to fit the non-weapon items, an unique mission must be found and accepted. After all required items are collected, crafting is crafting can be undertaken at any time. This is achieved via the Inventory menu (Return-2-1-3 through sidebar, or <shift>-I).

Installation of engines and shields

in order to fit the shields and weapon, an unique mission must be found and accepted. Once items are crafted for missions, each the item must be taken back to the respective NPC (so don't accept offers from soon-to-be hostile stations!). At which point, you can sell the crafted item or ask for the equipment and you'd be directed to an NPC mechanic who can fit it to the Skunk.

---- Spoiler ----

Ancient Relic Collection locations (see here for bigger spoilers (in-zone locations))

Kha'ak Relic Collection locations (see here for bigger spoilers (in-zone locations))