( This post will be updated with pertinent information - and as such does not cover every episode so far )
Five years after disappearing during the Battle Over Earth, a woman known as Maria Vega infiltrated Pioneer Station and unleashed a new threat upon the Federation. Backed by a mysterious organisation, with agents supposedly placed within Starfleet and the Government, Vega has worked in secret to develop an army of heavily modified Borg drones. Combining Halkonian and Telosian technology, these drones are capable of receiving direct instruction and disguising themselves by means of holographic filters capable of deceiving preliminary sensor analysis.
Having locked down Pioneer, Vega revealed a legion of these drones aboard the station coinciding with the arrival of a Borg Sphere seemingly under her control - a Sphere which had been briefly sighted by the crew of the Starship Athena four years prior. Forced off the station, with the attempt to retake her ending in disaster (with the destruction of the Starship Hera), Captain Mason and her staff fled to Starbase 215 to regroup and devise a strategy to neutralize Vega and her drones.
The investigation in to a missing starship led to the early revelation that the Vega Drones are in fact the crew of the USS Gibraltar, having succumb to a modified assimilation virus. Fleeing from the scene of the downed ship, the away team (to which Captain Mason was absent) were forced to put down on the moon of Rajusca and take refuge within the abandoned research facility on site. Their position was compromised by a drone that had slipped aboard their craft and attempted to assimilate Chief Engineer Craig McClintock.
McClintock was saved, but only through use of the last remaining sample of the Halkonian nano-virus in the crew's possession - designed by Halkonian scientist, Denara Clarke - which the science and medical teams had hoped would be key to disabling the Vega Drones. If they could reprogram the virus, it could be used to fight back.
Aboard Starbase 215, Captain Mason was contacted by a man currently referred to as 'The Truth.' He revealed that Vega was part of a conspiracy surrounding Starfleet's occupation of the Accobar System and it was suggested that he had a part to play in Mason's quick and timely requisition of a new starship - the Helia. When Mason was reunited with the away team and her crew was reassembled aboard their new ship, they set out to investigate Vega's actions and learn what she was planning.
With the political ramifications looming, President Olivia Taylor has decreed that the true nature of the threat currently residing in the Tyrella Sector be concealed from public knowledge until such time Starfleet has expended all immediate avenues of attack. Mason's crew ultimately came to realize that they would need to attempt to track down Denara Clarke in order to resume work on modifying a virus of their own. Starfleet Command and President Taylor agreed that a second attempt would be made to retake Pioneer and the Accobar System should Clarke be located and a counter-attack be developed.
During the final phase of the search, Captain Mason succumb to a degenerative neurological condition which had affected her decision making and fueled her obsession with learning 'the truth' about the Accobar conspiracy. After she was relieved of command by her second in command, James Menden, Mason collapsed and was forced to undergo extensive surgery at the hands of Doctor Rogan in order for her life to be saved. Upon awakening, Mason was able to access a blocked memory from a conversation she had with Vega before Pioneer was lost - and she realized that Vega was using the drones to search for something across the quadrant and beyond.
Once the Helia located Denara Clarke's cruiser, the Orion and Menden took an away team to meet with Clarke. Having shown the ability to influence and control individual drones following his assimilation, Clarke took an immediate interest in McClintock and posed that he would be the key to their developing a counter-virus. Sure enough, after two weeks of work, she would go on to propose to Menden that McClintock should undergo a full, but controlled assimilation using their own virus. With the Helia-side team seemingly hesitant to the idea, Clarke returned to the Orion to 'consult' with McClintock - but instead took her ship and jumped away with McClintock, Layton and Doctor Rogan on board.
As the Helia attempted to pursue, Mason, tired of being out of the loop, summoned Costello and Etis to Sickbay through means of Doctor Toshiro Ihilzu. Though they would not take much persuading to assist her, Mason chose to remind Costello and Etis of times her rash actions would go on to save their lives. Having "convinced" Ihilzu to cooperate, the three officers accompanied Mason to the Bridge, where she declared her intention to retake command. Having little choice, with Mason deemed fit for command, but also seeing how the current crisis was arguably worse than the one Mason presided over, Menden stepped aside and the crew got to work on searching for the Orion.
Lieutenant Etis picked up an anomaly on sensors. A floating mineral processing facility, deemed to be decommissioned, was very much lit up and active. The Helia arrived on the scene, to find no sign of the Orion. Knowing that she would most likely be cloaked, Mason decided to play Clarke's game and instructed Menden to lead a well-equipped away team to the platform to investigate. Beaming down, the team split up and scouted the platform until McClintock was located - alone and in distress. After warning that 'they' were coming, Menden noticed that a fresh puncture wound had pierced McClintock's neck. Before they could act, the team's location was suddenly under siege by Vega Drones. Outnumbered, with the drones adapting quickly to their weapons fire, they were quickly surrounded.
McClintock, however, was able to get to his feet and briefly find his composure. In this time, he stepped forward to the advancing drones and closed his eyes. One by one, the drones began to halt their advance and leave the area - followed by all the remaining drones following suit. His work done, McClintock collapsed on the spot and the team set up their pattern enhancers to re-establish a shaky transporter lock with the Helia and beam back to their ship - seemingly under attack.
The Helia engaged the Vega Sphere and was soon rejoined by the Orion. Together, the Starfleet and Halkonian cruisers were able to ward off the sphere. Having observed McClintock's abilities, Clarke returned Mason's remaining crewmembers and departed - allowing the Helia to return to Starbase 215 to prepare for the assault on Accobar. The crew regrouped and enjoyed a social gathering, with McClintock accepting that his sacrifice may be called upon in the battles to come.
The following day, the Tyrella Task Force assembled and a plan of attack had been agreed upon. Leading the charge, the Helia took point and the fleet jumped in to Accobar. At first, there was a disturbing lack of resistance as the fleet was able to enter the asteroid field and approach Pioneer. However, concerns aired from Menden and Etis proved valid as the Accobi defense grid was brought online - it's shield trapping the fleet and its cannons opening fire. Facing an onslaught of weapons fire, there was no hope of escape and little hope of resisting for long. However, hope arrived in the form of the Orion, which was able to bring down the shield by destroying a number of its emmiters from the outside. In retaliation, Vega had all of the weapons platforms target a single ship - obliterating it almost instantly. Mason negotiated a cease fire under the pretense of hearing out Vega's terms - handing over herself and McClintock.
Instead, it was agreed that the assault had to go ahead. The Orion, with Clarke having an Accobi interface to rival Vega's, would hold back and disrupt Pioneer's control over the weapons platforms while the fleet dispatched its boarding parties to breach the hanger bay. The plan was set in motion and the crew was able to board Pioneer and begin a sweep of the station. The Promenade, Engineering and Operations were secured, with no sign of Vega - while only a minimal compliment of her drones were encountered. However, with the boarding party separated, the station's lockdown procedure was enacted and Vega announced that the assimilation virus had been released. As the team succumb to its initial immobilizing effects, Vega revealed herself to McClintock - who she was forced to fight off using the Accobi device in her possession. Promising that they would meet again, Vega beamed out with Mason and over to the Sphere which made a quick flyby of the station before jumping away.
When the crew came around, they immediately set about accomplishing two primary objectives: securing the station's largely compromised systems and neutralizing the assimilation virus (spearheaded by Layton and Rogan respectively). Both tasks took their toll with the station fighting back against them - requiring the fusion core to be ejected and primed for re installation - and the crew deteriorating from the virus. However, having spent years investigating the nano-virus at its core and now armed with Denara Clarke's original specifications, Doctor Rogan was ready to test his cure - on himself. Securing a huge victory, the procedure was a success and the multispectral radiation procedure was expanded to include the entire boarding party.
With Pioneer deemed safe, a less-than-impressed Commodore Mason arrived from SB215 to assess the aftermath of the mission. In the Science Lab, Etis received a message of unknown origin, presenting a set of coordinates familiar to some aboard the station. It was that of a location near to which the Vega Sphere was first sighted a number of years prior. With nothing else to go on, Menden was prepared to take the Helia to investigate. The Commodore signed off on the mission, but noted that due to the unusual circumstances the Helia would have to travel alone.
Believing that a clandestine approach would work in their favour regardless, the Helia was prepped and departed under orders to capture Vega alive at all costs.
Update - 09/04/16
Updated.