Background
Incorporating mercenary companies and Holy Orders can be incredibly useful for a player. Not only does this provide exclusive access, it also cuts down the cost of hiring them by a large percentage
This guide is mainly deals with vassalizing mercenaries, since Holy Orders tend to be far easier to subjugate. It is valid as of patch 2.0.4.
Step 1: Acquire Island County[]
Mercenaries must be landed before they can be declared war on. In order for them to be landed, they must be baited into attacking the player (i.e. hiring them and dropping to a negative gold balance).
There are two immediate concerns for this: (1) They use an invasion CB which gives them an entire kingdom and (2) interference by strong vassals can easily prevent the turncoat mercenaries from winning.
A solution to this problem would be to conquer a county on an island belonging to a kingdom in which the player has no other land in. This way, the player would only lose one county and the mercenary army would be largely isolated from the outside world. Good locations to use are: Gotland, Shetland, Canary Islands, The Balares, Iceland, Sardinia, Corsica, Crete, and Cyprus.
Step 2: Invite Claimants[]
In order to subjugate a landed mercenary company, it is important to have a courtier with a strong claim on the mercenary title. This part is usually easy as claimants of the same religion group are not particularly resistant to being invited. If there aren't claimants available, consider assassinating the current title holder or wait a while.
Step 3: Prepare Army[]
It is absolutely essential to have an army capable of defeating the full force of the mercenary company intended to be incorporated into a country, as well as enough ships to carry it across water.
Step 4: Set the Stage[]
Hire the mercenary company and put its armies in the island county acquird in Step 1. Then squander all your money on construction/gifts and put your gold balance to red by raising all personal levies and ships. If player is lucky, then the mercenary company will rebel and declare an Invasion on the Kingdom title of the island county. If the mercenary company does not do that (i.e. just leaves), then repeat Step 4 or reload.
Step 5: Wait for Loss or Win Completely[]
Recent patches rendered it impossible to surrender (unless you have 100% war score, in this case they'll be forced to accept your demands even if your demand is to surrender) to mercenary companies prior to -100% war score. As a result, one would have to wait for them to slowly achieve victory. This is also where the one island county criterion becomes important. Since with that county being the player's sole possession in the Kingdom, its occupation by the mercenary would trigger the ticking warscore since all the player's possessions in that kingdom is technically occupied
Step 6: Enforce Claim[]
If your title claimant is still alive, immediately declare war on the mercenary company to enforce his claim. This is the part where a strong army is important, since the player needs to defeat the mercenary army and occupy its holdings. With recent patches, this is made more difficult since attacking from ship would guarantee at least 50% drop in morale (and remember we are attacking an island county).
However, people reading this guide are likely powergamers so this would just be a minor obstacle.
Step 7: Victory[]
Once warscore reaches 100%, give a county to your claimant and accept surrender. Congratulations! The mercenary company is now your loyal subject!
Step 8: Pure Cheese (Optional)[]
Instead of simply vassalizing a mercenary company, it is possible go one step further and take that mercenary title for the player character. To achieve this, do everything in Step 7 during pause. After that, assassinate all his successors (usually none) first and then him.
This trick is an abuse of the fact the claimant's mercenary title would become Agnatic-Cognatic Gavelkind at the very instant it is added to him. And with mercenary claimants having very little (if any) immediate relatives, the player character would usually be left as his sole successor (thus giving the player the mercenary title).