Squad Wars are a new addition to Star Wars: Commander. They are basically like clan wars in Clash of Clans or world wars in DomiNations. Two squads are matched up against each other and try to take out as many bases as possible. Whoever end up with the most up links destroyed wins. Uplinks are basically just their version of stars. There are some key differences between the games, for example, in Star Wars: Commander you can attack more than 2 times and you can attack the same target multiple times.
There are also NPC outposts which you can attack and if you defeat them you get special buffs for the whole team. It’s a fun game and I hope they keep adding to it and keep using the Star Wars theme to do it.