Originally a Thuranin star carrier, The Flying Dutchman became a mainstay of Humanity's efforts to survive in a galaxy full of danger. In the beginning, it alone and a Merry Band of Pirates was all that there was to stop other species' efforts to enslave and conquer Earth. During these travels it underwent a number of iterations which are explained below.
The section(s) below SCHMAYBE includes Spoilers.
The Flying Dutchman v1.0
The Flying Dutchman is described as being a very long ship which can been see in orbit of the Earth with the naked eye.
Since it it a star carrier it has the capability to jump long distances without the need for external resupply, although this doesn't mean it can operate without overhaul at Thuranin shipyards.
The Thuranin who are deeply suspicious of their client species the Maxolhx, install manual secondary control centers in their star carriers to prevent hacking.
The secondary control center is described as almost cathedral like gothic architecture with tactile switches everywhere to control everything. The Thuranin don't use this part of ship very often due to them controlling their ships with their cybernetic implants.
The Pirates installed a Mess Hall and exercise equipment in the ship once it had returned to Earth to allow them to feel more comfortable in the ship; other modifications include full size beds.
The ship is equipped with a medical bay which is stocked with medical nanotechnology.
Due to the many battles it has withstood, there have been a number of considerable modifications to the ship.
The Flying Dutchman v2.0
The Dutchman was ambushed by a group Thuranin destroyers, their damping fields caused the Dutchman's jump coils to fall out of sync, this and the fact that Skippy the Magnificent ejected some of the fusion reactors left the ship in a damaged state.
The ship was rebuild and cobbled back together by Skippy using parts from the Flower and exotic matter created with ad hoc particle acceleration in the mess hall ("I built this ship out of moon dust, stupid monkeys" - Skippy).
Changes to structure
Several ship docks were removed leaving just three at the center of the ship; it also had its spine shortened considerably. While the original had 6 Thrusters, v2.0 now only has 2. The front of the ship appears to be unchanged, from the outside anyway. 
It has at least three reactors as Skippy decided it might be funny prank the engineers by making it seem like reactor No.3 is melting down.
Reactor No. 2 was damaged. After Skippy was overcome by the virus the ship's systems began to break down one by one. 
Dr. Mark Friedlander came up with the idea to break the Jump Drive into coil packs to allow short jumps without all of the coils falling out of calibration. The downside to this was each coil pack burnt out when used.
Skippy was appalled once Nagatha Christie brought him back at the job "the monkeys" did.
Death of a Ship
The Dutchman after jumping into the Roach Motel system was sheared in half by the forces of an Elder Guardian. All that remained was the forward section and the Thuranin comm station lifeboat attached to a docking port.
The Dutchman had the be towed away from a collision course with the Roach Motel's star using dropships.
The Thuranin relay station lifeboat was used to provide barely enough power to give basic life support but it's energy was later used to energize the shields to prevent damage from the star. 
The Flying Dutchman v3.0
Birth of Frankenstein
It was repaired using parts of junk from destroyed ships in the Roach Motel's debris fields.
The ship is a Frankenstein ship and Skippy the Magnificent states more than once that is duct taped together and held together with a prayer.
The middle spindle has been completely removed along with the 3 remaining central main ship docks. Additionally, each of the 2 Thrusters are now of differing designs.
The Dutchman v3 has only 2 reactors that are ancient but serviceable for the needs of the Merry Band of Pirates.
The new shield generator is way more powerful than the original and can't even be fully charged at present.
The Dutchman was almost taken over by a US Delta team and Skippy's escape pod was destroyed by MASER fire.
The ship's armament are 2 MASER cannon's, a range of missiles but still no railgun. Skippy took the reactor out of the ship for repairs whilst the crew had down time in an abandoned Elder system.
The Dutchman received battle damage and wear and tear due to the Pirates taking her out without it being properly overhauled to reinforce the new parts from Gingerbread.
The ship also used its entire complement of missiles in the attack on the Maxolhx ships, in the complement of missiles were three ship killers, during this engagement the Dutchman almost lost the use of its normal stardrive because of the wormhole trap. Only due to Skippy having a monkey-brained idea did the ship destroy a Maxolhx ship with the MASER cannon.
The Flying Dutchman v4.0
After using the wormhole "bagel-slicer" on two Maxolhx Extinction-Class Battleships and one Maxolhx Heavy Cruiser, some parts of the ships were used to upgrade the Dutchman.
The Dutchman v4 now has 3 Maxolhx Thrusters and a Maxolhx Jump Drive from the heavy cruiser. It is powered by 3 reactors with Vacuum Power Modules (VPMs) to boost the power. The shield generator has sufficient power to be fully charged.
The ship's armament was the same as v3.0 but with a replenished number of ship killer missiles. Additionally, v4 gained 4 railguns, 2 MASER cannons and 2 point defense cannons all mounted on the front.
During the mission to acquire the first of the two Maxolhx Extinction-Class battleship, 4 of the Special Tactics Assault Regiment (STAR) team perished in the assault. Capt. Katie Frey injured her leg on this mission.
The Dutchman was not fully powered and required VPMs to bring the shields to full power. Valkyrie required more VPMs than the Dutchman in order provide more power for the armaments and reactors.
This was the same mission in which Major Fal Desai and Captain Renee Giraud, who were original members of the Merry Band of Pirates, were both killed in action. Additionally, Gunnery Sergeant Margaret Adams and Lt. Col. Jeremy Smythe were severely injured.