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Machine Spirit (MS) is by far the most valuable resource. It can be converted to any other resource (though you should never do this), speed up recruits/upgrades, and certain purchases can only be done with MS. The best use of MS is re-rolling hero talents as this can only be done with MS.
It may be tempting to use MS to speed up troop replenishment, but you should avoid getting into this trap. Instead, find ways to attack bases with fewer units or using solo heroes. If the cost is really low (e.g. 1 MS) and you need that troop (e.g. to skirmish), then it's OK. Never use it to speed up upgrades.
Many players use MS on greater rallies at the scriptorum. This is a reasonable use of MS but generally not worth it. The heroes you get can mostly all be obtained from lesser rally. There are a few heroes (Horus and Angron) which can only be obtained from greater rally. So if you really wish to get those heroes it may be worth it for you.
Machine Spirit is obtained from glory tournaments and from accomplishing daily missions. Sometimes a special cache will appear on your map. You can also purchase MS directly or watch ads to get MS.
Tip: Periodically, special events will come up when hero re-rolls cost less or are more likely to produce high-level talents. It is strongly recommended that you save up your MS for these events as they can significantly boost how much you get (at least 2x) from this precious resource.