INFECTED - SPACE
Your team's first task in the space portion of this mission is to defeat the Borg patrols in the area (a Cube and some spheres). Once that is complete you will need to destroy the Gateway and secure the system of all Borg ships. There are two Nanite Transformers on each side of the Gateway. Each Nanite Transformer has four Nanite Generators around it. The Nanite Generators heal the Nanite Transformer, and the Nanite Transformers heal the Gateway. There are also Borg ships with the word "Nanite" in their name, these also heal the Nanite Transformers.
The Strategy: There is an optional objective of completeing the mission within 15 minutes in order to get a bonus in your rewards. You will fail this objective if time runs out or if a Nanite Borg ship heals a Nanite Transformer. The best chance you have at completing this is by working as a team. Start by attacking the Borg ship which is above the Nanite Transformer (either a Sphere or a Cube depending if you are playing on Normal or Elite). Next, bring the health of the four Nanite Generators to 10% and wait. DO NOT DESTROY THEM YET. After they are all at 10%, as a team, destroy them all at once. Immediately attack the Nanite Transformer until it is destroyed. Clear the Borg ships from the area then do the same thing on the other side.
Afterwards a Borg Tactical Cube will warp in. I recommend taking out the remaining Borg ships then destroying the Borg Cube, followed by destroying the Gateway. You can also have four people attack the Cube while one person attacks the Gateway. When the mission is complete fly over to the station to pick up your reward. Congratulations!
INFECTED - GROUND
The entire purpose of this mission is to secure Starbase 28. Start by walking out of the transporter room and speaking with the nearby Starfleet officer. Now continue through the base and basically defeat all the Borg you see. Do not forget to remodulate your weapon using the free remodulator that you can get in your replicator (get it before the mission). The base is divided into three sections, each one blocked off from the next until you complete the necessary tasks.
The first task is to find the Starbase Director named Captain Ogen (who is now assimilated0 and defeat him. The basic idea here is to destroy the Borg who are in the room first then have the entire team focus fire on Captain Ogen until he is defeated. At one point he will put up some sort of "shield" which will stop you from attacking him for a few seconds. After that you can continue the assault uninterrupted. I should also mention at this point that there is an optional objective of save 10 Starfleet officers throughout the station. Doing so will give you an added bonus in your reward.
After defeating Captain Ogen continue through the base until you reach the final room and Manus of Borg. This room can be a little difficult so be prepared. The floor of the room is covered in plasma which will kill you almost instantly so stay away from it. Also, if your entire team dies, you will need to restart this room from the beginning.
Start off by having the entire team run up the ramp onto the center platform and defeat the Borg here. Now two team members should stay in the center platform and attack the rest of the Borg in the room one corner at a time. They should now move from the center platform, only attack from here. The remaining three members should go to the first corner of the room by walking over the walkways.
Each corner has a center terminal and three consoles around it. Once the Borg are defeated on a platform the three team members should stand by each console and activate them at the same time. This will lower the shield of the terminal and allow you to upload a virus. A progress bar will appear above this terminal, if it fills up then the shields will raise on this terminal and you'll have to come back to it and do this again. Go to each corner of the room and repeat the same steps: clear the Borg, use the 3 consoles, upload the virus.
Once all four viruses have been uploaded return to the center platform. If there are any Borg in the room defeat them FIRST. Once they are defeated, destroy the Shield Generator in the cente rof the room. Now Manus of Borg will come out and it is time for your team to defeat her. There are two methods to completing this:
METHOD A: Have your team spread out on different platforms around the spot where Manus is. This should prevent everyone from getting hit by her chain attack which causes damage to anyone nearby. Keep attacking her with everything you have until she is defeated.
METHOD B: The entire team should converge on the center platform and through everything you've got at her. If a team member dies then quickly revive that person. Continue until successful.
Once you are done, collect your reward which appears in the center platform. Congratulations!
The only thing in the space segment I have found is that once the transformer is down and the remaining ships destroyed, it is better for the group to meet on the opposite side of the gate away from the cube and take the gate down first.
The gate actually has offensive cabability itself which hampers the attack on the cube. The Cube remains stationary if you do not aggro it.
The most effective weapon to neutralize the Cube is the Klingon Carrier with Power Siphon drones, allowing more offensive ships to move in for the kill.