The word confederate has two main meanings:

1. A person who joins with others to work toward a common goal, especially in a formal alliance or agreement. When colonies or states become confederates, they agree to cooperate while keeping their independence. During the American Civil War, people from the Southern states that seceded were called Confederates because those states had formed the Confederate States of America, a confederation that fought against the United States from 1861 to 1865.
2. Someone who helps another person carry out a plan, often secretly. A magician might have a confederate in the audience who pretends to be a random volunteer but is actually helping with the trick. If two students work together to break a rule, they are confederates in mischief.

Notice that a confederate relationship involves cooperation between parties who remain separate, rather than merging completely into one. The term itself is neutral, simply describing people working together, though history shows that what confederates choose to unite for matters enormously.