Explore the Docks is a mission in Up Your Arsenal, taking place in the research facility, Daxx. Dr. Nefarious and Lawrence beamed a transmission on board the Starship Phoenix, which Al traced back to planet Daxx. Sasha Phyronix sent Ratchet and Clank to explore Daxx' research facility, and Al noted that the facility had two high-security terminals. One of these was in the islands, which could be reached by exploring the docks.
"Explore the Docks" is one of two missions that can be completed on Daxx upon arrival, the other being "Infiltrate the Weapons Facility". From where your ship lands, it is also possible to complete an optional segment near the start, that will allow you to obtain the Charge Boots and the Plumber trophy. At the end of the path for this mission, a titanium bolt can be acquired.
"Explore the Docks" is commenced after using the Hypershot to cross and then taking the path right, using the Hypershot again. The first section of this mission is purely a platformer segment, so do not worry about weapons straight away. At first, cross the set of versa-targets and platforms with the Hypershot, until you eventually see the Warship warp in.
As it does, the Warship will fire missiles that will destroy some of the platforms, with the target reticule for the missiles being visible on the platforms. Simply run past them, and then wall jump up at the next area and proceed forward. Once again, on the next set of grey platforms, the Warship will appear and fire missiles, so keep running forward before they can destroy any. You will reach the top of a structure, where the next path is to go right.
Use the Hypershot to create green platforms and then swing across. Hop across the next grey platforms quickly before the Warship destroys them, and just proceed forward with the Hypershot. You will see a group of green platforms together that need to be activated all in a row before proceeding forward.
The rest of this segment is fairly linear until you reach a long stretch of grey platforms clustered together. Avoid the missiles as before, and eventually you will reach a safe platform, with a teleporter back to your ship as well as a Gadgetron vendor. As the next segment is a boss battle against the Warship, consider purchasing any weapons you haven't previously purchased. Though likely unaffordable, the Annihilator is excellent against the next boss, while any other weapons are decent. When you are ready, take the Hypershot across to fight the Warship.
The Warship's main attack is the same seen previously: it will fire missiles, with a reticule on the ground indicating where its missile will hit, making it easy to dodge (provided you are not standing on one of the outer grey platforms). Its secondary attack is to use a laser beam, or beams, that sweeps across the ground, which must be jumped over. All its attacks do considerable damage, but they can all be dodged by jumping. In between its attacks, it will warp to a different position, making it crucial to follow where it goes. The attacks also increase in intensity.
The Warship is vulnerable to most weapons, with the exception of melee weapons due to its distance. The Miniturret Glove can also be useful to provide supplementary fire to the weapon of choice used. The most important thing for the battle is to dodge the attacks, and continue to lay down fire. Eventually, the Warship will fall. As with most bosses, consider saving the killing blow for any weapon you want to level up in particular, as the weapon that scores the kill will gain the most experience.
After this, use the Hypershot across to the next tower to commence a cutscene. A taxi will take you back to your ship. If you have not already completed it, it is a good idea to complete "Infiltrate the Weapons Facility" while still on Daxx; otherwise, head to the Annihilation Nation for "Meet with Courtney Gears".