Well, energy weapons are expected to vaporize battlesteel at a million and a half kilometers through heavy shielding. There's some serious power behind those things in case you feel like boiling off the oceans (relatively slowly) or slagging cities, even with the atmo interfering. As far as missiles, a multi ton object at over half light speed is going to leave one fuck of an impact crater. It is entirely possible for a spaceship to commit a Class 4 Apocalypse (destruction of the biosphere) upon a planet.
There are many treaties and agreements that are in place out of mutual self interest to prevent indiscriminate, wholesale, and wanton* bombing to reduce mass casualties. When it becomes clear that the defenders' continued resistance cannot affect the outcome of the situation (like, no friendly fleet can possibly make it in time, for example) they are obligated to surrender those defenses. This doesn't mean total abject surrender, it just means the game has shifted to where they're killing each other like civilized people. If the planetary government does NOT surrender, then you are absolutely free to start blowing up major cities until the people decide to fly the white flag and lynch any politicians remaining.
There's some rules and stuff as to what a valid military target is, and what right to self defense the planet has. For example, if there were to be an Antiship Missile Launcher in Central Park, New York City is therefore a valid military target and the responsibility for civilian deaths is on the heads of the administration that decided to put in their defenses in an urban area. The Pentagon is a valid target, the White House is a valid target, a power plant providing energy for military applications is valid, etc. A demonstration strike on Baltimore would be out, blowing up factories is out, so on, so forth. If a ship is blown up near the planet and most of its wreckage slams into Los Angeles, well, that's too bad for Los Angeles.
Hypering in ships and doing a missile drive by on a planet is absolutely and totally out, and if you're on the hook for a violation of this rule, you are not protected by it.
Defenders are only supposed to fire back at valid targets, and there's some context. An assault shuttle with Marines to capture San Francisco's military bases would absolutely and unquestionably be a fair target for Fighter Jets, but one landing in Sacramento, CA that is not participating in combat and is moving to secure the city is not valid because it's basically shooting at the police. A Fighter in atmo is absolutely valid, so on. Once they land, enemy Army/Marines/etc can indeed go against them, but civilians are expected to not resist with violence, so on. Like... in theory it is absolutely legal for a hidden tank to wait for the dropshuttle to land, the first soldier to exit, and then open fire, but the surrounding city blocks are probably going to get a surprise visit from Captain Cluster Bomb in response.
* Wholesale means civilian casualties which go beyond the collateral damage associated with legitimate military operations as defined under the laws of war. Wanton means that those casualties were inflicted deliberately, or that prudent precautions to prevent them from happening were not taken. The attacker is required to take precautions to prevent "accidents," and assumes that if such an "accident" occurs anyway, then adequate precautions were not taken. Which means that even if the attacker controls near-planet space, and has summoned the planet to surrender, and elected to bombard specific, legitimate military targets, he had better make damned sure that his "legitimate" bombardment doesn't get out of hand. Presumption of guilt, not innocence.
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The Honor is not as time sensitive. If you tell the Monarch that you need some time, the Monarch will nod in understanding and start recruiting military to occupy the planet. He'll wait for a bit, but not too long. There's other mercenaries.
The Takeover is a "If you don't move within a week or two, you'll be too late."
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I figured both. Your personal Armsmen or Knights or whatever will have a good bonus for the purposes of combat rolls, and the other Marines will have a small bonus in combat rolls to reflect the increase in quality of tactics and leadership. I figured "Extra space is used to fit the elite units", more or less.
Yes, you can absolutely do so. If you want to use your Fighters to shuttle missiles from your civvie ships to your warships, you can do it. If you want to unload all Combat Marines and gear onto a single ship (temporarily) you can do that as well.
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Shouldn't be. It'd been updated every single time.
Edit: OH I SEE IT WHOOPS LOL