Don't get me wrong. He's still totally an alien, but he's not operating under the orders of any greater alien authority. Eros is just some paranoid schizophrenic alien who got it into his head that human beings were on the verge of developing some bizarre superweapon that makes absolutely no sense outside of his own personal delusional cosmology, and decided to take matters into his own hands (perhaps even convincing himself that he *was* on a secret mission from the alien government). He stole a flying saucer and an alien device capable of raising and controlling the dead and landed in the middle of the first cemetery he came across once he reached earth, with only a very faint idea of what his imaginary "orders" said he was supposed to do to stop their imaginary "plan". Listen to the way he rants in the climax. Is that the talk of a trained captain of the flagship in a massive invasion fleet on an important mission to save the galaxy, or a very disturbed individual with a hero complex and a cheap resurrection gun who thinks he's the only one who knows what's *really* going on and is willing to do anything to stop it? Only three people in only one town were raised because "Plan 9" was the work of a lone nutjob, not an invading army.
The other flying saucers sighted during the course of the film are not part of Eros's fleet, but rather, alien authorities attempting to locate and apprehend him. The only reason they don't shoot him out of the sky is because Tanna is on board. Eros had fixated on her in his delusion, who in his mind was a trusted fellow agent incognito to avoid alerting the humans, and abducted her (probably believing he was "rescuing" her from something or other) so she could help with "their" plan (which she did, albeit under duress). If Jeff and the police hadn't busted into the saucer and foiled his scheme, Tanna would've eventually worked up the courage take advantage of her control over the resurrection device and turn the zombies on her captor (which may even be what she was attempting to do when she made Tor Johnson burst in).
- So who's The Ruler if Eros is an insane rogue?