In the aftermath of a battle, what is the chance that a pilot is captured? For example, what happens to clan pilots captured by the inner sphere? What is the chance / probability that an individual warrior is captured, and is automatic that they become (and except) bondsman to an inner sphere house / merc unit? I ask because my players are currently fighting through Operation Bulldog, and I wonder what will happen to the pilots of the clan mechs that they capture. Will they automatically join the Inner Sphere? Will the players merc unit be allowed to keep them, or would the House unit they are contracted to claim them?
It really all depends on a lot of things. You can track all of this through a game quite easily, it just gives you a bunch of other tokens.
For any mech equipped with a while head ejection system, forget it. They are designed to return to base, with or without pilot interaction. For mechs without that feature, old rules stated that a mechwarrior would eject into the hex immediately behind the mech, and could move one hex per turn, during the end phase. These units do not use initiative.
If the mechwarrior links up with a friendly unit, they are home free, if they are caught by a hostile unit, they are captured. You could complicate this with the friendly unit must withdraw off board, or to the edge of the board, to off load the mechwarrior, same for hostile units.
Clan mechwarriors are a curious thing, I'm pretty sure you have to win the battle to be able to claim isorla, including bondsmen. There are, however, canon sources that contradict this, such as CGB capturing Ragnar Magnusson, despite losing the trial.
Ultimately it's up to you, contrary to the opinion of at least some members of this board, canon states that captured clan warriors are a largely docile lot, and will simply serve with whomever captures them. Unless your mercs have specific clauses in the contract, PoWs will be at the discretion of the merc commander, as the IS does not traditionally consider PoWs as salvage.
If you want to provide further hooks for your campaign, you could have the ISF being very interested in clan PoWs, you could parley this into a link up scenario, or into a breakthrough scenario if the ISF simply tries to take the PoWs.