The way this works internally is that 3-4 mission controllers key skills are averaged together with the hardware reliability and astronauts skill (which controllers, which astronauts, which skills, and so forth is determined by the step being performed), and a random number is generated from 1-100. In this game, however, mission control gets a "saving throw" each time a failure occurs - if they roll low enough, then the failure is a "minor glitch, fixed" or "minor glitch, mission can continue" and all is well. As you might expect, BARIS had a reputation for being "impossible". There was nothing that the player could do beyond maximizing hardware reliability and then cross their fingers (max HW reliability in BARIS was 98%, but this was practically impossible to achieve - most of the time you were required to launch at 86-90%). In BARIS (the predecessor to this game), that was all there was - there would be failures, and the consequences of those failures would be catastrophic or not based on a look-up to an internal table. On top of all that, most missions will have a step reliability far below 95% (indeed, ~85% is much more common), so. And these are EASY missions - a Gemini DA (the simplest lunar landing mission, in terms of steps) has 21 steps, while an Apollo landing has 28 steps. The probability of success on one mission (11 steps, 95 % reliability) is 0.95^11 = 0.5688 = 56.88% - roughly 1 in 2. If we assume that the reliability of each of the steps was 95% (and that's grossly optimistic), the odds of 100% (55 success in 55 attempts) success for all of these steps is 0.95^55 = 0.05954 = 5.954 %. Each of these missions has 11 steps so (as of the 1Q 1964) there have been 55 Mercury steps attempted. For example, as of 1964 Q1, the walk-through shows 5 Mercury missions (1xmanned suborbital, 2xunammend orbital, 2x manned orbital) listed. This is expected even with highly reliable hardware (~90%), and the reason is basic probability math. Each of these glitches could have been (but wasn't) a catastrophic failure that would have set the program back at least a quarter, and likely much more than that (depending on how long it took to re-fly the failed mission). As you read through the walk-through, you'll see a large number of "glitches" after successful launches.
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