There is an old game entitled Dark Colony [1997]. Exemplary gameplay HERE against multiple, basic level AI forces. Similarly to Halo Wars, the base could only be built at fixed locations, with special carrier ships used to summon further facilities. The units seen in the gameplay with many types of bars and stars over their heads are the chiefs. There are various ranks of them that can be assigned for the skirmish mission or that are given in the campaign. Chiefs are more powerful than regular troopers, also are capable of calling in reinforcements - that is in case of humans - or causing the abduction of enemy units by a sheer UFO, which is valid for the aliens [Taars], whom the humans fight. Basing on appearance, humans are inclined towards cybertechnology, while Taars have gone the highly evolved psi-organic route.

There are various kinds of units that can be researched and manufactured - more or less symmetrical for both sides - supported by weapon and armour level upgrade options, in a manner typical for a real time strategy game. The battle is primarily for the resources collected at the gaysers, minable with the use of specialized harvesters. The game features the day and night cycles, with humans being more active and seeing further during the day time and aliens taking over analogous features in turn during the night time. What is introducing a bit of variety to this otherwise plain wargame is the presence of ancient civilizational artifacts, recoverable also with the use of the harvesters. Some of these artifacts - with powers applicable in warfare - are easily controllable, some are chaotic, dangerous both to friend and foe alike.

Dark Colony does have quite an eerie atmosphere, implying the mystery and the terror of facing extraterrestrial enemy unknown [UFO [1994] pun intended] on a hostile semiterraformed Martian ground. Was Dark Colony an inspiration for Halo Wars, basing on similiarity of certain elements, such as chiefs presence and bases - supported with starships - buildable only at fixed locations? Wonder how Dark Colony 2 would look like if it took the place of Halo Wars, to be developed instead.

In the manner of trivia, here are descriptions of the usable artifacts one can recover in the Dark Colony - on the basis of gamepedia.com:
  • The Solaris is an energy harnessing device which has been modified to expel the power it stores. When activated, it begins to absorb all visible light within a 40km radius and then releases the energy in a massive energy blast that burns everything within a 50m radius.
  • The Maxtor is a "gravity well", quite similar to a black hole. When activated, this unit buries itself in the ground unfolding its five petals to reveal atomic attractors. Any unit caught within 25m of the gravitational pull of the Maxtor gets dragged into the processing chamber and is pulverized into space dust.
  • The Lunatek emits ultrasonic waves that induce a hallucinatory state of fear in both organic and non-organic [cyborgized] units. Units affected by waves become paranoid and delusional, attacking anything and everything in sight. The grunts on Mars call this uncommon medical condition "berserking".
  • The Kaox. This spherical unit is believed to be an ancient butchering machine. When activated, the Kaox drops to .2m above the ground and opens up to reveal a vast array of whirring carbonic blades that shred everything within its path. The Kaox' main drawback is that it moves in a random pattern and once activated, kills anything [it encounters].
  • The Tektaara is a mind control device that causes the victim to become a willing puppet of the whoever controls the Tektaara. Due to their advanced intelligence, humans and Taar are immune to the Tektaara, but the indigenous species of Mars are not. Deploying the Tektaara gives the player unlimited control over all the Martian creatures currently active on the world.
  • The Portalis. [Lack of description, name suggests a portal of some kind, answer probably in the campaign.]
  • The Esgaard. [Lack of description, lack of idea, answer probably in the campaign.]
The difference in the UI makes me think that there's no way that this game at all inspired Halo Wars.

Ensemble actually started out the development of Halo Wars with the idea that there would be non-static base building. After a bit, they realized that static bases fit the console limitation better. A big reason for that was to make the maps more dynamic (less flat plains, more chasms and mountains) and provide players with the ability to snap to their predetermined bases with the D-pad in the absence of the ability to simply click on the mini-map. If anything, they came to the idea of static base locations through trial and error rather than taking inspiration from a little known game from 1997.
The difference in the UI makes me think that there's no way that this game at all inspired Halo Wars.

Ensemble actually started out the development of Halo Wars with the idea that there would be non-static base building. After a bit, they realized that static bases fit the console limitation better. A big reason for that was to make the maps more dynamic (less flat plains, more chasms and mountains) and provide players with the ability to snap to their predetermined bases with the D-pad in the absence of the ability to simply click on the mini-map. If anything, they came to the idea of static base locations through trial and error rather than taking inspiration from a little known game from 1997.
Butterfly effect. You saw it, you remembered the pattern, you kind of liked it or thought it could be useful if applied somewhat in a different manner. You maybe forgot the title, you felt like the similarity is vague, but the pattern is there, right in your game. Nobody will prove a heck, because hey, this is also not the point, but still we could ask whether maybe there is some aware connection or just a coincidence. But despite static base, there are chiefs, there are those spaceships assisting and stuff. I liked the night and day thing, it seems to be exclusive to DarkColony, could be a good thrill factor if given better emphasis. Mind also there is a decade of difference and active industry progress between DarkColony and HaloWars, so hard to expect any direct resemblance in case there was yet a thing.