The alarm system on the bike is one of the worst features according to one engineer on the project. The unit can mysteriously fail and the batteries on the key fobs can die. This system can be removed or simply bypassed by installing a key switch.
If you are intending to bypass the alarm because you believe it is faulty, first triple check that it's the alarm that's causing issues. Take off your seat by undoing the two bolts, then remember to pull up on the front while sliding it forward. Identify the alarm module, pictured here.
Follow the wires towards the front of the bike and disconnect the alarm module. Identify the two wires you're interested in on the harness: red with a white stripe + yellow. Take a spare piece of wire or a paperclip and bridge these two wires on the harness side.
When you do this, the bike should turn on.
If the bike does not turn on, the problem is not the alarm.
If the bike does turn on, try reconnecting the alarm to make sure the alarm module still does not work. If the Metacycle still works with the alarm module connected, the problem could have been related to excessive heat.
Order a replacement part first. The alarm module is held in with sticky tape. Disconnect the wires from the harness at the plug, then just pull really hard to pry off the module. Keep this part around until the new unit is working, since sometimes they come with a different end - you might need to splice the new unit's wires to the old unit's plug.
This video shows one Metacycle owner installing a three-position switch and replacing the alarm module. With the switch in one position, the alarm works. In another position it bypasses the alarm.
Drilling is required because the original alarm and power button will continue to work with the key in one position.
If you also bridge to the alarm's pink wire (the harness's blue with white stripe), the light on the power button will be enabled as well.
Bypass the alarm system by bridging the alarm's orange (harness's yellow) wire and the alarm's red (harness's red with white stripe) wire with a switch. This Facebook video demonstrates it working.
Facebook post with links to two different key switch options and lots of pictures. If you're installing a key switch this way, a 20 mm diameter switch fits without drilling.
Facebook post with a video showing that a key switch with red and orange wires bridged works.
If you'd like to bypass the alarm without splicing wires, look for DJ7065F-2.2-11 connectors. Attach your own wires between a keyed switch and the replacement connector.