Here is a FAQ on Retrofit ships as taken from Here.
Season 2 Retrofit Ships
* Long Range Science Vessel retrofit; similar in appearance to the U.S.S. Voyager / Intrepid Class; it has Ablative generators (increased armor) though it can only fire torpedoes while that power is active.
* Exploration Cruiser retrofit; similar in appearance to the U.S.S. Enterprise D / Galaxy Class; it can perform the dramatic Saucer Separation which has been seen in movies and on television. This turns you into an escort with a saucer pet that fires phasers on your target.
* Tactical Escort retrofit of the Defiant Class; similar in appearance to the U.S.S. Defiant; it has cloaking capabilities for the utmost in stealth and punishing weaponry.
Klingon Empire Retrofit:
* Kar'Fi Carrier, a Fek’Ihri Tactical Carrier with kamikaze S'Kul Fighters.
Main method for earning a Season 2 Retrofit Ship
Free Ship Token
Each Federation Captain earns 1 Free Ship token, which they may spend to commission one these ships when they reach Vice Admiral rank. Each Klingon Captain who obtain the rank of Lieutenant General will also receive 1 free ship token. These tokens function just like the free ship tokens that you have gained at lower ranks. Meaning you must visit Admiral Quinn (Fed) or Chancellor J'mpok (KLG) when prompted by your promotion mission.
These Ship Retrofit requisition options are not visible until you are Vice Admiral Rank/Lieutenant General Rank.
Remember that the ship you commission this way is only available to the Vice Admiral/Lieutenant General that completes the transaction via a Ship Requisition NPC. Alternative characters on your account will need to decide what ship they will claim once they reach Vice Admiral/Lieutenant General. Their ship selection does not have to be the same as what your first Vice Admiral/Lieutenant General claimed.
Note - As there is only one Klingon Retrofit ship, this is the only way for Klingon Lieutenant Generals to claim their Season 2 Retrofit Ship.
Alternative methods for obtaining the Season 2 Retrofit Ships
You can earn and collect each of the Federation Retrofit Ships for each of your Vice Admiral characters!
Federation Vice Admiral Emblems
In addition to the free ship token you receive for reaching Vice Admiral Rank; as you perform Daily Missions of appropriate level to your Vice Admiral, you will be rewarded with Emblems. These Emblems may be used to purchase additional Retrofit ships for the Vice Admiral that has gathered those emblems. You will be able to make this purchase through the same vendor that already distributes Emblem rewards.
Federation C-Store Purchase
For those of you who are seeking to unlock additional ships without spending your Emblems, you may purchase a Retrofit ship through the C-Store. A C-Store Retrofit purchase is made through the C-Store via a Vice Admiral and will only complete if that Vice Admiral has an open ‘Commissioned Ship’ slot available when you attempt the transaction.
If you do not have an open ship slot, the transaction will not complete, and your Cryptic Points will not be taken. Before you are able to complete this C-Store purchase, you will need to free up a ship slot by either discharging one of your other ships, or you could purchase additional ship slots through the C-Store.
If you purchase a Retrofit Ship through the C-Store in this way, it will be automatically placed in your ship list; it will also unlock the Retrofit for your entire account. When an alternative character reaches Vice Admiral, they will be able to claim this C-Store purchased ship from the Ship Requisition NPC. This ship purchase WILL NOT appear under the 'Special Unlocks' tab.
At this time the Klingon Faction has only one Retrofit available. You will be able to use your Free Lieutenant General Ship Token to claim it.
If you like the idea of obtaining all of the Retrofit Ship for all of your Vice Admiral Federation faction characters; you may do so via any combination of the options listed above.
For example, you could purchase two Retrofit ships via the C-store, Tactical Escort and Exploration Cruiser, unlocking them for all of your Federation characters of the appropriate level. To obtain the third and final ship, each Vice Admiral would then use their free ship token to claim the Long Range Science Vessel. This would result in access to all of the current Retrofit Ships.
Be Careful! Customer Service will not able to refund or reset any accidental or unintended purchase of a Ship Retrofit. Use caution and be careful when selecting the ship Retrofit that you want, you will not be able to un-make your choice. Meaning if you purchase a ship through the C-Store that you have already acquired through one of the other methods it will not undo one of your previous choices.