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I am curious how often imperium armies actually fight against eachother. For example, I know that GK and SM often kill guardsmen that have seen daemons, and that the DA and SW have some feud going on. However, I am curious how often the other armies fight. With it being on of the most played armies, a common scene in GW stores is the SM player fighting another SM player. As far as fluff is conserned, do Space Marines really ever fight eachother? How about Inqusition/SoB/GK against Marines? SoB vs Inquisition/Marines? The list can easily go on from here.

I know about the Heresy, and that there are often defectors to the Tau and Possessed Guardsmen, but those aside, do loyalists ever fight loyalists, or is that just a scene for the gaming store due to the popularity of Marines and the fact that four armies in the game are all members of the imperium?

I'm certain some inquisitor has ended up fighting Blood Angels after accusing them of heresy. Dark Angels will kill other imperial servants to keep their secret safe. Ordo Malleus is nuts.

http://www.garbled.net/40k/red.scorpion.history.html

Go to the above link to see the history of the Red Scorpions, pretty bloody. It's hard to find another group in the Imperium that they have met and not fought against exept maybe the GK's. Each chapter of SM has a certain amount of autonomy afforded to it and as such they deside for themselves what the "Will of the Emperor" is. So it's easy to see how so many different people all claiming to act in the name of the emperor would clash a lot...you know, kind of like modern religions.

The usual way of explaining it at my local is as a training exercise, although the Grey Knights codex has an entire section on why they would fight anyone. Included in the list is that "the other guys are possessed/are using possessed items" and "we don't like the way you fight/your principles/the way your chaplain preaches/your face"

Its all training.

The most clubs and stores don't have much armies to lend or the person refuses to use
anything he's not familiar with.

In the game its not uncommon to go imperium vs imperium.
In background its possible to start a fight over nonsense,but the great number of players would make fluff-only settings a problem.
You cannot force your opponent to play non-imperial because you refuse to go against natural allies.

IMHo the loyalists fight not other loyalists,but ancient differences can overthrow sense and its always possible to have
a battle from friendly fire.

Well in DoW: Dark Crusade the SM fought the IG because they refused to leave when the Necrons and Chaos came to the planet, and in Soulstorm the SoB fought the SM and IG because they thought they were tainted, and the SM fought the IG because they refused to leave it to real men.

There are tons of reasons the Imperium would fight among itself:
Political - There are millions of Imperial armies stretched throughout the galaxy. It wouldn't be unheard of for planetary governors, Imperial Generals, Barons/Dukes/Counts of various regions fighting over power.

Military reasons - like Cheese pointed out, conflicting orders to take/destroy/guard different objectives could lead the Imperiums forces to fight eachother because of miscommunication and beaurocracy that causes them to get different orders.

Long standing animosity - Different SM chapters, Inquisitors, Sisters, etc may have long standing rivalries.

Mistake - Two forces may think the other to be chaotic or rebelling or something.

Actual rebellion/chaotic influence - Guard/Marines may actually corrupted in some way.