@GreenGoatCurrently, there are a number of factions within Arcadia.
First, there's the Imperium;
While that sounds like a grand title, it's effectively just a ragtag group of heroes lead by the God Emperor of Man, Nova. While Nova is currently searching for a Terminal, a device that would allow him to travel between worlds and potentially return everyone to their homeworld, the rest of the team is running from the Alliance of Conquerers.
The Alliance of Conquerers;
A group of Big Bads from across the Multiverse, working together with the goal of conquering all of reality. The Original team consists of Bowser, Ultron, Queen Gamora and Sachiko. They were recently joined by Starkiller and Kars. They're the closest thing to a main antagonist in the story as of yet, and definitely not friendly.
The Aliens;
Led by the Ethereals from Xcom, this group has the goal of attaining knowledge and power. They're not specifically evil, but they're also far from 'good guys', and not very friendly to outsiders. They recently captured a Doomsday clone, whom they're holding in captivity.
The Goa'uld Empire;
An empire of interdimensional proportions, which seeks to conquer all in veneration of their God leader person, Ba'al. While they've only just showed up IC, they have the potential to become a main antagonist.
The Inkvaders
An incredibly odd group consisting of a squid girl, a different squid girl, and a psychotic magical Esper with the goal of eliminating all of reality. They plan on "Inkvading" the world. This is probably the silliest group, but also one of the most amusing.
Plot-wise, nothing's really shown up. Basically just protagonists and antagonists at this point. Nova & co versus the Alliance of Conquerers and the Empire, with the Aliens kinda sitting at the side. There are also a bunch of loose canons running around, including a Daemon Prince, a priest, and several others.