One of the most frequent requests that I have heard since we started presenting Inside Beta: Star Trek Online, is for more specific information about the kinds of missions in the game, so I thought I'd use this time to go into a little bit more depth.

First, I should say that I appreciate the way that the STO designers went about creating the missions for their game. They have been put together in such a way as to insure that players don't easily get bored of what they are doing, alternating between ship, space and ground missions.
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So, in thinking about the best way to present the kinds of missions that are available in Star Trek Online, I thought I'd take the time to recount a few of the ones that I experienced:

SS Azura

In the first mission that I undertook, I was sent to the aid of a Federation cargo ship called the SS Azura. The Azura is under attack by Orions. My first order of business was to fend off the attackers. This was your more typical "destroy all attackers" objective. After completing the space combat portion of the mission, I learn that the ship has suffered heavy damage, numerous plasma conduits have ruptured and that they have been boarded. Like a good Starfleet Ensign, I beam over to the ship with my away team to help out.
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Once on board the Azura, I see damaged systems and unconscious crewmen. I scan the nearest crewman and learn that he's been overcome by radiation from the leaking systems and that I can beam them to my ship's sickbay as soon as I get those leaks fixed.

My away team and I make our way through the ship, interacting with the appropriate consoles to shut down the leaks which have been blocking us off from the Captain in Main Engineering. Once we shut down the leaks, we are able to beam injured crewmen away and make our way to Engineering.

Upon arriving in Main Engineering, we find that the Warp Core is too heavily damaged and is going to breach, so we have to fight our way back to our beam-in point to return to our own ship. Once back on board, we are hailed by an Orion battleship. Bigger and more powerful, it tells me to back off or be destroyed. I fight the battleship, which basically equates to a small "boss fight" before beaming the captain and remaining crew from the Azure to safety. Mission complete.

Miners

Players who wanted to see some emphasis put on diplomacy will be happy to learn that there are indeed missions that involve no combat at all. The first of which I came across sent me to a mining colony that had been having problems with their workers.
Star Trek Online

Upon beaming down to the planet, my away team and I were greeted by the colony's leader who told me that they were willing to talk, but felt that Starfleet just didn't understand their plight. He urged me to go and speak with some of the workers so that I might educate myself as to their problems.

Speaking with the miners, I learned that there were a number of grievances. In fact, everyone seemed to voice something different. Like the seasoned MMO vet that I am, I ignored their answers the first time around in favor of checking off the "speak to so-and-so" instructions in my quest log. When I returned to my original contact though, he wanted to test me to see if I understood the miners' plight any more or if I was like the rest, and didn't understand at all. He asked me a series of questions to which I didn't know the answer and basically told me to kiss off. The next time through with another character, I took the time to listen (read the dialogue) and answer the questions correctly. It was a mechanic that surprised me, I don't mind saying.

Species 8472

Yup, your favorite race from fluidic space makes a return in one of the game's early missions that sees you escorting a Vulcan diplomat from Earth Station to a monestary on the planet P'Jem.
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When your ship arrives at the planet in question, you are hailed by a Klingon ship that tells you that you are carrying an impostor and while your puny Federation might not see the truth, the Empire does, and you will be destroyed. This sets up a nice pace battle with the Klingons.

After the battle, you beam down to the planet, which is under siege by Klingons. You have to fight your way to the top of a large hill to rescue some captured Vulcans, only to learn that the Ambassador was indeed an impostor, a member of Species 8472. Your merry chase looking for the creature sets up more Klingon combat on the ground before I lost the creature's trail. One of my bridge officers helpfully informed me that he detected transporter activity, and that we should return to our ship.

Lo and behold, the creature had beamed back up to its ship, which was far too powerful for my beginner ship to handle. My orders were to hold it off until help arrived (via a timer).

Patrols

Some of the earliest mission types that players will receive are patrols. Starfleet is spread thin, what with their war with the Klingons and trouble with the Orions and others, they ask you to take yourself and your ship on patrols of various systems. For example, you might be asked to Patrol the Vulcan System, the system actually consisting of a number of destinations, each one producing a different circumstance.
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Still, this article is about the different kinds of missions that are available, so I'll tell you a little bit about three missions I undertook while on patrol:

1. Miners came to the forefront again in a quick combat mission as they were being attacked by Orions. Being my badass self, I popped in with my ship and blasted 'em out of the sky.
2. You find an Orion Shipyard and are tasked with fighting your way through guard patrols and destroying a number of the monstrosities. It's a great one to group up for, as two-ship or more tactics are quite effective.
3. A transport ship near a mining base is having trouble with its navigation system in an asteroid field. You have to find the ship and escort it to safety. Not the most entertaining mission I've ever played, but it did offer an interesting variation.

Now, this is just a small cross section of the missions that are available to players in Star Trek Online. As I said at the top, I have been both impressed and entertained (for the most part) by the diversity of things that are available for players to do, and by the way that the missions mix it up enough so that I don't feel like I'm grinding my enemy's bones to make my XP.

It's not all roses and sunshine though, missions like the escort mission mentioned above don't feel like they have much meat on them, but the mechanic required (escort a vessel) has potential if used later in the game in a mission that asks you to escort a vessel while defending it from attack. So, as you might expect from a beta, things are still a little bit rough around the edges at times. However, the general approach and the tools that Cryptic has at their disposal give me hope that the missions will become increasingly deep and dynamic as the game progresses toward launch.
Source: Star Trek Online : Inside Beta: Missions - Star Trek Online for PC at MMORPG.COM